Actually, I just realized something that's even nastier. When I filed my 1040X, I didn't request any of the overpayment refunded to me and elected to have it all applied to my 2020 estimated tax.
When I called the IRS, I asked if I could still apply this to my 2020 tax, and was told I couldn't and I had to wait till the matter was settled but could apply it next year. So now I'm actually out doublle my original overpayment.
It looks like I made a mistake thinking that "amount of claims" listed on the IRS letter is the IRS saying I need to pay that amount back, when it probably meant the IRS Is saying this is the amount of refund in question which they are denying...
I don't know if the fact I applied a payment to my 2019 taxes will cause a complication for me in trying to apply it instead to my 2020 return. I've always done my taxes but it looks like I may need professional help to sort this mess out.
