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Ask the community...

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Hey Cedric! I went through something very similar with my 2019 taxes last year. The good news is that once you receive the partial disallowance letter, the IRS has already made their determination and your adjusted refund should be processed relatively quickly. In my case, I received my $450 adjusted refund about 3 weeks after getting the letter. Since you mentioned it's for a business expense deduction (I saw your comment below), those typically process faster than credit-related adjustments. The IRS usually deposits these payments using the same method you chose on your original return - so if you had direct deposit set up, it should go to the same account. One thing that helped me was checking the letter for any specific processing codes or timelines mentioned in the fine print. Sometimes they include estimated processing dates that aren't obvious at first glance. If it's been more than 4-6 weeks since you got the letter, definitely call the number printed on it - those specialized lines are usually much better than the main IRS number.

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That's really helpful to know about the business expense deductions processing faster! I'm actually in a similar boat - just got my partial disallowance letter yesterday for a 2020 return where I overclaimed some home office expenses. It's reassuring to hear that 3 weeks is a realistic timeline. Did you notice any status changes on the IRS website before your refund actually showed up, or did it just appear in your account without warning?

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Jamal Carter

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@Abigail Spencer - Great question! In my experience, the IRS website Where ("s'My Refund tool" didn) t'show any updates until literally the day before the money hit my account. For weeks it just showed my original refund status, then suddenly updated to show the adjusted amount with a deposit date. So don t'worry if you don t'see changes online right away - that seems to be pretty normal for partial disallowance situations. The actual deposit just showed up as IRS "REFUND in" my banking app without any advance notice beyond that final website update.

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I just went through this exact situation a couple months ago with my 2019 return! Got the partial disallowance letter in January and was so confused about what would happen next. In my case, it took exactly 19 days from when I received the letter to when the adjusted refund hit my bank account. Mine was also for a business expense issue - I had claimed some equipment purchases that the IRS couldn't verify with the documentation I provided. The thing that stressed me out was that there's really no way to track the progress once you get that letter. The "Where's My Refund" tool on the IRS website didn't update until the very last day, and even calling didn't give me much additional info beyond "it's processing." Since you mentioned your issue is also with business expenses, you're probably looking at that 2-4 week window everyone's talking about. The silver lining is that once they send you that letter, the hard part (their review and determination) is already done. Now it's just a matter of their payment processing system doing its thing. Hang in there - I know the waiting is nerve-wracking, but your money is definitely coming!

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Has anyone here actually gotten audited by the IRS for premium tax credit issues? I'm in a similar situation but honestly thinking about just claiming the credit for all months and seeing what happens. It's only about $340 for that overlap month and seems like a lot of hassle to figure out.

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KylieRose

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Don't do that! The IRS gets reporting directly from both your employer and the marketplace about your coverage. They specifically look for this kind of overlap. My cousin tried what you're suggesting and got a letter 6 months later demanding repayment plus a 20% accuracy penalty. Just report it correctly upfront.

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Zara Khan

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I went through almost exactly this situation last year and can confirm what others have said - you'll need to repay the APTC for that overlap month. The IRS considers you ineligible for the premium tax credit during any month when you were eligible for qualifying employer coverage, regardless of whether you actually used both plans. A few practical tips from my experience: 1. Make sure to check your employer's plan documents for the exact eligibility date - sometimes it's different from when coverage actually starts 2. Keep documentation of when your employer coverage began in case the IRS asks for proof later 3. The repayment caps mentioned earlier can really help limit what you owe if your income qualifies One thing that caught me off guard was that my tax software initially missed the overlap entirely until I manually entered the employer coverage dates. Double-check that your software is accounting for both coverages correctly when calculating your Form 8962. The good news is that even though you have to repay that month's APTC, you can still claim the premium tax credit for the other 6 months where you only had marketplace coverage. It's frustrating but not as bad as having to repay everything!

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This is really helpful, thank you! I'm dealing with a similar overlap situation and your point about checking the employer plan documents for the exact eligibility date is something I hadn't thought of. Did you end up having to pay any penalties beyond just repaying the APTC? And when you say your tax software initially missed the overlap, do you mean it didn't prompt you to enter employer coverage dates, or it just didn't calculate the repayment correctly even after you entered the information? I'm using TurboTax and want to make sure I'm not missing anything that could cause problems later.

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Has anyone actually gotten FreeTaxUSA to correctly calculate the tax credit for income tax withheld on 1042-S? I tried reporting it as suggested here but my refund calculation seems off.

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Natalie Chen

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Make sure you're entering the withholding in the Federal Payments section specifically as "Other Federal Withholding" rather than with your W-2 withholding. I made that mistake last year and had to file an amendment because FreeTaxUSA didn't apply the credit properly.

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Emma Taylor

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I went through this exact same situation two years ago! As a tax resident filing jointly, FreeTaxUSA definitely works for 1042-S reporting, but you need to be careful about a few things that haven't been mentioned yet. First, double-check that your 1042-S shows the correct tax treaty benefits applied (if any). Sometimes universities mess this up even for tax residents. If you see treaty benefits applied when you shouldn't have them as a resident, you'll need to contact your university's payroll office to get a corrected 1042-S. Second, when entering the fellowship income as "Other Income" on Schedule 1 Line 8z as Chloe mentioned, make sure to also check if any of it qualifies for the American Opportunity Tax Credit or Lifetime Learning Credit. Fellowship money used for qualified education expenses can sometimes still allow you to claim these credits for other educational expenses you paid out of pocket. Also, since you mentioned HSA contributions - fellowship income actually counts as earned income for HSA contribution purposes, which is great news if you're trying to maximize your HSA contributions for the year. The combination of FreeTaxUSA plus getting official IRS guidance through something like Claimyr (as Sophie mentioned) is honestly your best bet for peace of mind on a complex situation like this.

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Connor Byrne

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Has anyone considered the Lifetime Learning Credit instead? It's not a business deduction but it's worth up to $2,000 per year for qualified education expenses. Definitely not as good as deducting the full cost on Schedule C, but it's a guaranteed benefit if you meet the income requirements.

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Yara Elias

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The income limits are pretty low for the Lifetime Learning Credit though. I think it phases out completely once you hit around $90k for single filers? Most MBA students probably earn too much to qualify.

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Based on my experience as a tax professional, the key issue here is the timing and business connection. Since you launched your entrepreneurship venture during your MBA program, you're in a gray area that the IRS scrutinizes carefully. For Schedule C deduction eligibility, you'll need to demonstrate that: 1) Your business was actively operating (not just planned) when you incurred the MBA expenses, 2) Specific courses directly maintain or improve skills you're currently using in your existing business operations, and 3) The education doesn't primarily qualify you for a new trade or business. Given your $6,700 in sales, you clearly have an active business, which strengthens your position. However, I'd recommend only deducting the portion of MBA costs that directly relate to skills you're actively using in your current venture - perhaps courses in entrepreneurship, marketing, finance, or operations management. Document everything: course descriptions, syllabi, and written explanations of how each course directly applies to your current business activities. Consider consulting with a tax professional before filing, especially given the audit risk Miguel mentioned. The safe approach might be claiming a smaller, well-documented portion rather than the full $37,000.

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James Maki

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This is really solid advice, thank you! I'm new to this community but dealing with the exact same situation. The documentation approach makes a lot of sense - I've been keeping all my course materials but hadn't thought about writing up explanations for how each class connects to my business activities. One question - when you mention "actively operating" versus "just planned," what kind of proof would satisfy the IRS? I had some early customer inquiries and was developing my product during the MBA program, but my first actual sale didn't happen until a few months in. Would business registration date, early email communications, or prototype development documentation help establish that timeline? Also wondering if anyone knows whether the IRS differentiates between core MBA courses versus electives when evaluating business relevance? I took several entrepreneurship electives that seem directly applicable, but I'm less sure about required courses like organizational behavior.

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I went through this exact same situation with TurboTax last year and can confirm what others are saying - it's completely normal but poorly explained. The key thing to understand is that your original return and amended return are processed as completely separate transactions by the IRS. Here's what actually happens: 1. Your original refund will be issued regardless of your amendment status 2. Your amendment creates a separate tax liability that must be paid independently 3. The IRS systems don't automatically "net" these amounts together One important tip that saved me stress: you can actually make the amendment payment using EFTPS (Electronic Federal Tax Payment System) directly to the IRS instead of through TurboTax. This gives you more control over timing and you can see exactly when the payment processes. Just make sure you include the correct tax year and form code (1040X) when making the payment. The whole process took about 6 weeks for me - got my original refund in 3 weeks, and the amendment was processed about 3 weeks after that. The separate payment thing is definitely counterintuitive, but once you understand it's two different systems, it makes more sense.

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Jason Brewer

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This is such a common source of confusion! I went through the same thing two years ago and it really threw me off. What helped me understand it better was thinking of it like this: your original return is like a contract you already signed with the IRS - they're going to honor that refund amount. Your amendment is essentially a new, separate contract saying "oops, I actually owe you more money." The IRS processes these through different departments and systems, so they can't just automatically adjust one against the other. It's frustrating from a cash flow perspective, especially for contractors like us who might be waiting on that original refund to cover the amendment payment. One thing that might help ease your mind: you can check the status of your original refund using the "Where's My Refund" tool on IRS.gov. Once you see it's been approved for direct deposit, you'll know exactly when to expect it. Then you can time your amendment payment accordingly (just don't miss the deadline as others have mentioned). The whole system definitely feels backward, but once you accept that it's two separate transactions, it becomes less stressful. Your original refund is coming - the amendment doesn't change that!

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This explanation really helps! I'm dealing with this exact situation right now and was getting anxious about the timing. One question - when you say "don't miss the deadline," are you referring to the original tax filing deadline (April 15th) or is there a different deadline for amended return payments? I filed my original return in February but just realized I need to amend for some freelance income, so I'm trying to figure out how much time I have to get this sorted out.

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