Here's another, simpler way of looking at it. It's the same as if you had not applied the 2020 overpayment to 2021 estimated tax. It's as if you got a refund of the 2020 overpayment, and wrote a check for a 2021 estimated tax payment. The 2021 estimated tax that you paid doesn't change. When you file the 2020 amended return, you have to pay back the excess refund that you got.
