Didn't the extension payment show up as a credit on your tax return? For 2020 Federal Extension payments should be on schedule 3 line 9. And go to 1040 line 31. It is included in your refund or reduces a tax due.
If you didn't enter it then the IRS should have added it in for you. Or eventually catch it and send it back. You have to ask the IRS about it. Do you have proof you paid it like your bank statement?
