You just need to amend your return(s) and return your refund to the IRS. If you amend and return(s) the refund, you should be fine.
You can use the steps here below to amend from 1040 resident return and file a correct 1040NR, TurboTax does support nonresident returns however we partner with Sprintax and they can help you with a 1040NR. You will need to go to the state website and locate their amended return form and print it and complete it. You can attach your correct nonresident state return to the state amendment before mailing. You cannot e-file an amended return.
After your 1040NR is complete, print your 1040NR with Sprintax; do not e-file it.. You must mail the 1040NR along with the amended return Form 1040X
Per IRS Form 1040X instructions, page 8:
To amend and file the correct return, do the following:
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Enter your name, current address, and social security number (SSN) or individual taxpayer identification number (ITIN) on the front of Form 1040X.
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Don’t enter any other information on page 1. Also, don’t complete Parts I or II on page 2 of Form 1040X.
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Enter in Part III the reason why you are filing Form 1040X.
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Complete a new or corrected return, Form 1040NR,
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Across the top of the new or corrected return, write “Amended.”
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Attach the new or corrected return to the back of Form 1040X.
**Make sure you check the box to show the tax year that you are amending on Form 1040X. Make sure you sign your 1040X and 1040NR.
Sprintax Form 1040X 1040X Instructions
To return your refund please see the attached link from the IRS: Returning an Erroneous Refund - Paper Check or Direct Deposit
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