It will reflect on the Form 1040-X amendment form.  If you end up with a refund by filing 1040-NR, IRS will send you the fund.  If you end up owing more, you will pay them back.  See instructions of Form 1040-X below.

If you have filed a Form 1040 and needs to amend by submitting a 1040NR, see steps below.  You would need to submit both the Form 1040-X and form 1040NR together.  To amend, please wait until your return is fully processed and you have received your refund or your payment has cleared.

• Download the Form 1040-X from IRS website (see below).  On the front page of Form 1040-X, enter your name, current address, and social security number (SSN) or IRS individual taxpayer identification number (ITIN)
• Do not enter any other information on page 1.  
• Do not complete Parts I or II on page 2 of Form 1040X.
• Enter in Part III the reason why you are filing Form 1040X.
• Complete a new or corrected form 1040-NR.  As TurboTax does not support nonresident forms, click here Sprintax.
• Across the top of the 1040-NR, write “Amended”
• Attach the new or corrected return (Form 1040NR) to the back of Form 1040-X and submit to the IRS.

https://www.irs.gov/pub/irs-pdf/f1040x.pdf  - form

https://www.irs.gov/pub/irs-pdf/i1040x.pdf  - instructions

(See page 6 under Residents and Nonresidents)