I also accidentally filed non-filer for 2019, and followed the advice on this thread to correct my error. This is my timeline:
May 2020: Accidentally filed non-filer
June 2020: Filed an amended 1040x paper return, with a cover letter explaining my error
June 2020: Made a payment for taxes due, ~$2500
....waited patiently...no update on my IRS.gov account....
February 2021: Received a paper check refund for ~$2500 (and no documents from IRS)
February 2021: (plan to) return the paper check to the IRS by mail marked VOID with brief explanation cover letter
I'm assuming the IRS has yet to process my paper return. I assume returning the voided check would be right thing to do.
Does this make sense, or does anyone have any advice?