Paper return filed but not processed by IRS yet. Payment due was submitted online to IRS on 7/15 and has now been refunded by check.

[awolfgang0519]

We were unable to file our 2019 return electronically due to a submission made to get our stimulus payment. (We were getting an error stating a return had already been submitted.) We followed the instructions from TurboTax to file our return via mail. We owed tax, and I made the payment on the IRS website on 7/15 so it would be on time. Today, we received our entire payment plus interest via check from the U.S. Treasury. I went online to the IRS website to find the status of our return, and according to the transcript on file for 2019, it shows a $0 return (due to the stimulus info filed). Any suggestions of what we should do?

[fanfare]

What instructions?  If you did not file Form 1040X or mark your Form 1040 with "EIP Amended Filing" in bold letters on top of the first page, this is what happens.

[awolfgang0519]

The 1040 was marked as EIP Amended Filing at the top, as you noted. 

[Critter-3]

Sounds like your paper return is still in the pile of unopened envelopes so until your return reaches the top of the 11 million plus pile the return will not be processed.  If you have not yet cashed the check I would hold onto it since they will be looking for the money eventually.  To avoid a late filing penalty you may need to send the check back which shows you did pay on time along with the proof of payment receipt you got from the IRS when you made the online payment.