Tax Court Strikes IRS Timeline for Partnership Adjustments – Houston Tax Attorneys


The partnership audit regime rules are not all that new at this point. But what makes them new is that the IRS hasn’t fully implemented them, is often not following the new rules, and the disputes involving this have just started to trickle up to the courts.

Practitioners are also at fault here. Many have not taken the time to review or understand these new rules. This is actually understandable, as there have been so many changes in the past several years. The incoming and outgoing administrations with their own tax agendas, followed by the IRS upheaval, has pushed this new set of rules to the side. But for those of us who work on IRS audits, appeals, and litigation, these rules are essential.

Partnership audits under the BBA follow a specific timeline that can determine whether the IRS has the authority to make adjustments to partnership tax returns. When partnerships submit modification requests to reduce their imputed underpayments, the question becomes: when does the clock start ticking on the IRS’s deadline to issue a final partnership adjustment? The Tax Court’s ruling in JM Assets LP v. Commissioner, 2025 WL 123456 (T.C. 2025), demonstrates what happens when the IRS fails to follow these timing requirements and shows how courts will invalidate Treasury regulations that contradict clear statutory language.

Facts & Procedural History

This case involved a limited partnership headquartered in Texas. The partnership managed real property investments.

In 2018, the partnership disposed of several properties. The selling prices ranged from $88,000 to over $7 million. The partnership reported these transactions as installment sales on its Form 1065 partnership return. The partnership properly disclosed these transactions using Forms 4797 and 6252 by providing detailed information about the five properties.

On June 9, 2022, the IRS issued a Notice of Proposed Partnership Adjustment (“NOPPA”) to the partnership to increase the partnership’s section 1231 gain by $5,499,437 and to calculate an imputed underpayment of $2,034,792. The IRS took the position that the partnership should have recognized the full gain on these property sales in 2018 rather than treating them as installment sales.

Following the established procedures for BBA partnership audits, the partnership submitted a Form 8980 modification request on February 14, 2023, seeking to modify the tax rates for two of its partners. The IRS approved the modification request in full on June 5, 2023. However, on December 1, 2023, the IRS issued a Notice of Final Partnership Adjustment (“FPA”) containing the same adjustments and imputed underpayment amounts as the original NOPPA.

The partnership challenged the FPA by filing a petition in U.S. Tax Court, arguing that the adjustment was untimely under section 6235(a)(2) of the tax code. The case involved cross-motions for summary judgment, with each party arguing different interpretations of when the limitation period began to run.

Understanding BBA Partnership Audit Procedures

The Bipartisan Budget Act of 2015 changed the rules of the game for how the IRS partnership audits are conducted. Under these procedures, for taxpayers who do not elect to opt out of the new rules, the IRS examines partnership returns and makes adjustments at the partnership level rather than examining individual partners. This centralized approach is intended to streamline the audit process, which it does in some respects. It also creates specific timing requirements that both the IRS and partnerships must follow, which makes it more difficult for the IRS and taxpayers.

When the IRS identifies adjustments to a partnership return, it calculates an “imputed underpayment” by applying the highest marginal tax rate to the net partnership adjustments. The partnership then has the opportunity to request modifications to this imputed underpayment, such as demonstrating that certain partners are tax-exempt or subject to lower tax rates. Taxpayers are often subject to lower tax rates.

About the Partnership Modification Process

The modification process under Section 6225(c) allows partnerships to request adjustments to their imputed underpayments after receiving a NOPPA. This process recognizes that the IRS’s initial calculation using the highest marginal tax rate may not accurately reflect the actual tax liability of the partnership’s specific partners.

Partnerships can request modifications for several reasons. They may demonstrate that certain partners are tax-exempt organizations that would not owe tax on their distributive shares. They may show that individual partners are subject to lower tax rates than the highest marginal rate used in the imputed underpayment calculation. They may also request modifications based on amended returns filed by partners or alternative procedures that would reduce the overall tax liability.

The modification request must be submitted on Form 8980, along with supporting documentation to substantiate the requested changes. The IRS has established specific procedures for these requests, including required forms and documentation that must be attached to make the request complete. The partnership has 270 days from the date the IRS mails the NOPPA to submit its modification request.

How Do Modification Requests Affect the Limitation Period?

The I.R.C. § 6235(a) limitation period determines when the IRS must complete its partnership audit and issue a final partnership adjustment.

This section provides several different time limits, and the IRS must finish its audit within the latest of these periods. The provision creates different deadlines depending on whether the partnership requests modification of its imputed underpayment.

Under I.R.C. § 6235(a)(3), if a partnership does not request modification, the IRS has 330 days after mailing the NOPPA to issue its final partnership adjustment. This provides a straightforward timeline that begins when the IRS sends the proposed adjustment notice.

However, I.R.C. § 6235(a)(2) creates a different timeline when a partnership submits a modification request. In this situation, the IRS has 270 days “after the date on which everything required to be submitted to the Secretary pursuant to such section is so submitted” to issue its final partnership adjustment. This language appears to start the clock when the partnership completes its modification submission.

When Is Everything Required Actually Submitted?

The central legal issue in this case involved interpreting the phrase “everything required to be submitted to the Secretary pursuant to such section is so submitted” in I.R.C. § 6235(a)(2). The IRS had interpreted this phrase through Treasury Regulation § 301.6235-1(b)(2), which defined the submission date as “the date the period for requesting modification ends.”

Under the IRS’s interpretation, even if a partnership submitted a complete modification request early in the 270-day period, the limitation period would not begin until the modification window closed. This interpretation was based on the theory that partnerships could theoretically submit additional information during the modification period, so the submission could not be considered complete until the period ended.

The IRS also pointed to Form 8981, which partnerships can use to waive the modification period, as evidence that the modification window remains open until formally closed. According to the IRS, the failure to submit Form 8981 meant that the partnership could make additional submissions during the entire 270-day period.

The partnership took the position that the statutory language was clear and unambiguous. The limitation period begins when the partnership actually submits everything required for its modification request. Since the partnership submitted its complete Form 8980 on February 14, 2023, and never submitted additional information, the 270-day period should have begun on that date.

The Court’s Analysis of the Modification Timeline

The U.S. Tax Court applied the Supreme Court’s decision in Loper Bright Enterprises v. Raimondo, which emphasized that courts must exercise independent judgment when reviewing agency interpretations of statutes. The court noted that statutes must have a single, best meaning that is fixed at the time of enactment.

The court found a direct conflict between the plain language of I.R.C. § 6235(a)(2) and the IRS’s regulation. The statute clearly states that the limitation period runs from “the date on which everything required to be submitted… is so submitted,” while the regulation interprets this to mean the date the modification period ends. The court observed that these are different dates, and the regulation must give way to the statute.

The IRS attempted to defend its regulation by pointing to I.R.C. § 6225(c)(1), which grants the IRS broad authority to establish procedures for modification requests. However, the court rejected this argument, explaining that even broad rulemaking authority does not extend to contradicting statutory text. The court cited Varian Medical Systems, Inc. & Subsidiaries v. Commissioner for the principle that regulations cannot change unambiguous statutory provisions.

The court examined the facts for the partnership’s modification request to determine when everything required was actually submitted. The partnership submitted its Form 8980 on February 14, 2023, requesting modification of the tax rates for two partners. The IRS never requested additional information during the modification period. The partnership never submitted supplemental materials after its initial request.

The IRS approved the modification request in full on June 5

The IRS approved the modification request in full on June 5, 2023, confirming that the initial submission contained everything necessary for the requested modification. These facts established that the partnership submitted “everything required to be submitted” on February 14, 2023.

Under the correct interpretation of I

Under the correct interpretation of I.R.C. § 6235(a)(2), the IRS had 270 days from February 14, 2023, to issue its final partnership adjustment. The 270-day period expired on November 11, 2023, which fell on a Saturday, so the deadline extended to Monday, November 13, 2023, under I.R.C. § 7503. The IRS issued its FPA on December 1, 2023, which was 18 days after the limitation period expired.

The Takeaway

This decision establishes that partnerships can rely on the plain language of section 6235(a)(2) when calculating limitation periods for BBA partnership adjustments. When a partnership submits a complete modification request, the IRS’s 270-day deadline begins immediately, not at the end of the modification period as the Treasury Regulation suggested. This ruling provides partnerships with greater certainty about limitation periods and demonstrates that courts will not defer to agency interpretations that contradict clear statutory language.

For partnerships that have received final partnership adjustments, this case serves as a reminder to carefully review the timing of modification requests and FPA issuances. The IRS’s failure to follow proper procedures can result in adjustments being thrown out entirely, even when the underlying tax positions may be questionable.

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Government agencies and non-profits often enter into business arrangements with private companies that, ultimately, are structured as a percentage of revenue. This approach frequently replaces traditional fixed payments like rent or management fees.

The typical example involves a building that a business owns and leases to a government agency or non-profit. The business collects a percentage of the fees or other revenues collected from the end users of the building in lieu of receiving traditional rent payments. The arrangement may also be structured as a management fee or labeled some other way.

There are also instances where the parties’ roles are switched, with the business being the tenant and the government or non-profit being the landlord. The central aspect of these arrangements is typically a type of revenue-sharing agreement. The rent or other payments may look more like business income to the business rather than rental income.

But what if the parties do not negotiate a fair deal or a deal that turns out to work economically? For example, what happens when the end users do not generate enough money to pay for the ongoing expenses of the business operationand the business advances funds to cover the shortfall? If this advancement is not paid back, is this a bad business debt and deductible as such? Or is it a capital contribution that adds to the business basis and cannot be immediately deducted?

The case of Anaheim Arena Management

The case of Anaheim Arena Management, LLC v. Commissioner, T.C. Memo. 2025-68, addresses this debt-versus-equity distinction and provides guidance on when business advances in revenue-sharing arrangements qualify for immediate tax relief.

Facts & Procedural History

AAM is a limited liability company that manages the Honda Center arena in Anaheim, California. It operates under an exclusive management agreement with the City of Anaheim.

The Samueli family owns AAM through a network of related entities. AAM’s management contract granted it the right to operate the arena and receive a share of residual profits. The agreement also imposed obligations to maintain the facility and cover operational shortfalls.

Between 2004 and 2015, the Honda Center consistently struggled to generate sufficient revenue to cover its expenses. The management agreement required AAM to make advances when the arena faced funding shortfalls. AAM ultimately advanced approximately $51.5 million in three categories: Operating Loans to cover day-to-day expenses, Debt Service Loans to meet bond obligations, and Capital Expenditure Loans for facility improvements.

Each advance was documented with promissory notes bearing interest at prime plus one percent. The notes designated “the Honda Center” as the borrower, even though the arena was merely a building owned by the City with no legal capacity to borrow money. Under the management agreement’s waterfall provision, AAM was to be repaid from arena revenues only if sufficient funds remained after paying higher-priority obligations.

By 2015

By 2015, it became clear that the Honda Center would never generate enough revenue to repay the advances. AAM claimed a $51.5 million bad debt deduction on its 2015 partnership return. The IRS conducted an audit and disallowed the deduction. The IRS also imposed accuracy-related penalties under Section 6662. AAM petitioned the U.S. Tax Court to challenge both the deduction disallowance and the penalties.

What Qualifies as a Bad Debt Under Section 166?

The tax code provides a deduction for business bad debts under Section 166. This allows taxpayers to deduct debts that become wholly or partially worthless during the taxable year.

The deduction is based on the economic reality that businesses sometimes extend credit or make loans that cannot be collected. The idea is that the tax system should not penalize taxpayers for such legitimate business losses by having the business pay tax on all of its income, given the financial loss that it incurred.

As with every deduction, there are nuances. Section 166 has requirements that taxpayers have to satisfy to claim bad debt deductions. The main requirements is that the debt has to become worthless during the tax year. For business debts, the deduction is treated as an ordinary loss rather than a capital loss. This treatment typically provides more favorable tax treatment since ordinary losses can offset ordinary income without limitation.

The regulations under Section 166 define the scope of deductible debts–adding more explanation. Treasury Regulation Section 1.166-1(c) states that “only a bona fide debt qualifies for the purposes of section 166.” The regulation defines a bona fide debt as “a debt which arises from a debtor-creditor relationship based upon a valid and enforceable obligation to pay a fixed or determinable sum of money.”

This regulatory definition requires more than just docume…

This regulatory definition requires more than just documentation labeled as a loan or promissory note. The substance of the relationship must reflect the characteristics typically associated with arm’s length debt transactions. Based on this, the courts examine whether the parties intended to create a genuine creditor-debtor relationship or whether the advance served other business purposes.

When Must a True Debtor-Creditor Relationship Exist?

When is there a true debtor-creditor relationship? According to the courts, this relationship must be based on a valid and enforceable obligation to repay a specific amount. The obligation cannot be contingent on business success or dependent on factors beyond the borrower’s control.

A valid debtor-creditor relationship requires several elements. The debtor must have legal capacity to incur the obligation. There must be consideration for the debt–meaning the debtor received something of value in exchange for the repayment obligation. The terms must be sufficiently definite to allow enforcement through legal proceedings if necessary.

The enforceability requirement means that the creditor must have realistic legal remedies available if the debtor defaults. If the purported creditor cannot pursue collection through normal legal channels, courts may question whether a true debt relationship was intended. This is particularly problematic when the purported debtor lacks assets or legal capacity to be sued.

Courts also examine whether the parties treated the arrangement as a genuine debt relationship. If the creditor repeatedly waives payment obligations, extends maturity dates without penalty, or subordinates repayment to all other business obligations, these actions may indicate that no true debt was intended. The behavior of both parties has to be consistent with a genuine lending relationship.

How Do Courts Distinguish Debt from Equity in Tax Cases?

Federal tax law has long grappled with distinguishing debt from equity in various contexts. The characterization affects not only bad debt deductions but also interest deductibility, dividend treatment, and numerous other tax consequences. Courts have developed multi-factor tests to analyze the economic substance of purported debt relationships.

The Ninth Circuit applies an eleven-factor test to determine debt versus equity status. These factors include the names given to the instruments, the presence of a maturity date, the source of payments, the right to enforce payment, participation in management, subordination to other creditors, the parties’ intent, capitalization adequacy, identity of interest between creditor and debtor, payment of interest only from earnings, and the ability to obtain third-party financing on similar terms. As it is a factor analysis, no single factor is determinative in this analysis. Courts examine the totality of circumstances to determine whether the advance represents a genuine arm’s length debt transaction or an investment in the business.

With that said, the more an advance resembles typical commercial lending practices, the more likely it will be characterized as debt. Conversely, advances that are subordinated to other creditors, lack enforcement mechanisms, or depend entirely on business success for repayment tend to be characterized as equity investments.

This type of debt-versus-equity analysis recognizes that business owners sometimes provide funding to their enterprises that, despite formal documentation as loans, function economically as capital contributions. The tax consequences differ based on whether the arrangement is debt or equity.

Tax Conseuqnces of Debt vs. Equity

The distinction between debt and equity can result in dramatically different tax consequences for both the advancing party and the recipient.

When an advance is characterized as debt, the advancing party can potentially claim a bad debt deduction under Section 166 if the debt becomes worthless. This deduction is available in the year the debt becomes worthless. Business debts receive ordinary loss treatment. Ordinary loss treatment allows the deduction to offset ordinary income without limitation. This can provide an immediate tax benefit.

For the recipient of debt financing, interest payments are generally deductible business expenses under Section 162. The principal amount of the debt does not create taxable income when received. This is because borrowed funds must be repaid. Upon repayment, the principal amount is not deductible. This represents return of borrowed capital.

When an advance is characterized as equity, the advancing party cannot claim an immediate deduction when the investment becomes worthless. Instead, the loss is generally recognized only when the equity interest is sold, exchanged, or becomes completely worthless under Section 165. This can delay the tax benefit for quite some time.

For partnerships and limited liability companies treated as partnerships, equity contributions increase the partner’s outside basis in their partnership interest. Losses from the entity can flow through to partners, but only to the extent of their basis in the partnership. This basis limitation can prevent immediate recognition of losses even when the business fails.

When the partnership or LLC is ultimately dissolved or th…

When the partnership or LLC is ultimately dissolved or the partner’s interest becomes worthless, the partner may recognize a capital loss equal to their remaining basis. However, capital losses are subject to significant limitations. Individual taxpayers can only deduct $3,000 of net capital losses per year against ordinary income, with excess losses carried forward to future years.

Corporate taxpayers face even more restrictive rules for …

Corporate taxpayers face even more restrictive rules for capital losses. Capital losses can only offset capital gains, with no deduction against ordinary income. Unused capital losses can be carried back three years and forward five years, but many corporations lack sufficient capital gains to absorb large capital losses.

Suffice it to say that this is an area where advance tax planning can help avoid unexpected tax liabilities.

How Did the Tax Court Analyze AAM’s Advances?

The tax court applied the eleven-factor test to AAM’s advances and found that none of the factors supported debt characterization. While the promissory notes were labeled as debt instruments, the court noted that the Honda Center had no legal capacity to borrow money. This made the notes largely ceremonial documents rather than enforceable obligations.

The court found that the maturity dates in the notes were meaningless because AAM could extend them at will and actually did so repeatedly. The source of payments was limited to arena revenues, creating uncertainty about repayment that differed from typical commercial debt. AAM had limited ability to enforce collection since repayment depended entirely on the arena’s financial performance.

Regarding management and participation, the court determined that AAM made the advances to fulfill its contractual obligations as arena manager and to preserve its profit-sharing rights. The advances were subordinated to most other arena obligations. AAM’s return included both interest payments and a share of residual profits. The court found this profit participation particularly significant in distinguishing the advances from arm’s length debt.

According to the court, the parties’ intent analysis revealed that the advances served AAM’s broader business interests rather than representing pure lending transactions. AAM needed to maintain the arena’s operations to preserve its lucrative management contract and profit-sharing arrangement. The court concluded that AAM made the advances as equity-like investments in the arena business rather than as a disinterested creditor seeking fixed returns.

The Takeaway

This decision explains the risks one takes in revenue-sharing arrangements and in advancing funds to cover operational shortfalls. Courts will look beyond formal loan documentation to examine the economic substance of these advances, particularly when the advancing party has contractual obligations to provide funding or receives profit participation beyond fixed interest rates. The case shows that advances made to preserve existing business interests or management rights could to be characterized as equity investments rather than deductible debt. This characterization can transform what appears to be an immediate ordinary loss deduction into a capital contribution that provides no immediate tax benefit and may only be recoverable as a limited capital loss upon disposition of the business interest.

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In 40 minutes, we’ll teach you how to survive an IRS audit.

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