To enter, change or delete a payment made with an extension request (Federal, State, Local) -
On the next screen select the type of extension payment made and click on the start or update button
Or enter federal extension payment in the Search box located in the upper right of the program screen. Click on Jump to federal extension payment
The federal extension payment will be shown on Schedule 3 Line 9. The amount from Schedule 3 Part II Line 13 flows to Form 1040 Line 31
I encountered this problem also. I filed for extension of my 2021 return, paying the additional tax I thought I would owe (using Turbotax to file the extension). I filed for an extension because I did not have all the official tax documents that I needed in mid-April. When I revisited the software months later after receiving all the necessary tax documents, I found that the payment made when I filed for the extension was reflected in my refund amount when I first opened the Turbotax, but disappeared later. I wasn't sure what happened. I eventually discovered that when I went through the interview the 2nd time (months after filing the extension), when I was asked if I wanted to file an extension, I said "no" (thinking that I had already done that). Saying no meant that for computational purposes, the amount I paid with the filing for an extension was not propagated through the forms/worksheets to the final 1040. I went back to that portion of the interview and answered "yes" to whether I wanted to file an extension. In doing so, the original payment I had made when I filed for extension was propagated through the system and properly credited on the 1040 (and of course in my refund amount...). The real difficulty with this problem was that one cannot enter the amount manually on the 1040 form directly (the data field goes back through numerous forms -- Schedule 3, 1040 Worksheet, Tax Payment Worksheet, to Form 4868 -- none of these can be edited directly!). So go back through thr interview and say YES to the extension question. Good luck!
When you requested your extension you were supposed to pay your estimated tax due. Did you enter the payment you made into your tax return? Go to Federal>Deductions and Credits>Estimates and Other Taxes Paid>Other Income Taxes