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I did a research internship in California in 2023 under a J-1 visa. Unaware of the fact that TurboTax is only for residents, I filed my taxes with TurboTax. I ended up getting a letter 5447C to confirm my identity, which made me realize I filed the taxes wrongly. So I mailed the correct 1040NR tax form in a 1040-X amendment.

The issue is that now, 5 months later, I got the refund deposited to my American bank account, which seems to imply they used the data from the original Form 1040, instead of the 1040NR/1040-X. The value of the refund is also higher than it should have been because of that.

So... now what? As I said, I already mailed the amended return (back in April) and it should have been received, according to the tracking number. So I'm not sure why they processed it using the old form instead. Should I send the 1040-X again, or what? And how would I return the extra cash they deposited?

This question seems to suggest I should have waited until the original refund was processed to then file the 1040-X, however, the 1040 was on hold due to Letter 5447C, so it did not make much sense to me.

I'd like to at least visit the US again in the future and I would prefer to not be in bad standing with the IRS, even as a non-resident :)

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You expected your amended return to supersede your original return. You thought someone would dig through the boxes of papers of the incoming returns in the IRS office, find the one you originally sent, and throw it away and put the amended one instead.

That's not how it works.

The amended return supersedes the original return, if accepted, but only after the original return is processed. Until then there's nothing to amend. The returns are processed by applying them to your account in the IRS computer. If there's no return on your account, then the amended return cannot be applied to anything. So by definition, an amended return cannot be processed before the original return.

Generally, when you prepare an amended return, you base it off of the original, and then calculate the difference. If the difference is in your favor - you're asking for a refund. If the difference is in the favor of the IRS - you need to submit a payment.

So consider the hypothetical situation:

  • A taxpayer submitted a tax return showing $1000 refund owed them.
  • A taxpayer then realized that they forgot to include income that resulted in additonal $2000 in taxes.
  • A taxpayer submitted an amended return showing the additional income and the difference in taxes resulting from it.
  • Since the taxpayer already requested $1000 refund on the original return, that amount goes to the 1040X line 18.
  • Since the difference between the original tax and the amended tax is $2000, that amount shows up on line 20.

The end result is that the taxpayer needs to send $2000 to the IRS, while also receiving $1000 from the IRS.

Should I send the 1040-X again, or what?

No, they will process the one you sent. Now that your original return has been processed, there's something to amend.

And how would I return the extra cash they deposited?

You need to submit a payment for the difference which should have been calculated on the 1040X (line 20). See here for different ways to submit payments, the best would have been to attach a check to the 1040X.

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    For IRS to issue the (TPP) notice the original return was at least in FOF and I believe also in IMF with a freeze code, so they don't need to search for paper (if it was even originally filed on paper; TurboTax would offer efile); but concur they don't throw away that original but instead post it as filed and then modify it according to the 1040X -- which (still!) requires manual handling that usually takes 4-5 months, so OP: don't worry if you don't hear anything quickly. Commented Jun 30 at 4:07

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