Why does TT want me to submit payment with amended return when I am still getting a refund?

[BayArea2020]

I made edits to my amended return and I am now trapped in a double-counting situation that I don't know how to fix.

I efiled with TT on 4/15 and my return has been accepted by the IRS.  I am now amending my return to remove an incorrect IRA deduction.  On my original 1040, my anticipated refund was enough to pay all of my estimated taxes for the year, and I applied all of the refund.  Now, my refund has dropped, but it's still enough to pay the first two quarters.

At first, TT still applied the original (higher) refund amount (that I am not longer getting?!) towards my estimated taxes, and I was worried that the ES vouchers for Q3 and Q4 will be wrong, leading to an underpayment.  On the screen where I specify the amount of my 2021 refund that is applied towards my 2022 estimated taxes, it now says that the max I can apply is the new (lower) refund amount, so I edited the value down, and the vouchers are now calculated correctly.  But then in the filing instructions, TT still wants me to submit payment for the "excess" refund amount with my 1040-X, even though the IRS never paid out the original refund to me, because I applied it to my estimated taxes. 

Going into forms view, I see on the 1040-X Line 20 where it says that I owe the IRS the difference between the two refund amounts, BUT that calculation is based on the idea that I received credit for the original refund amount, which means  TT should let me apply the original amount from my 1040 to my estimated taxes, right?  But when I try to go back and edit the refund amount that I am applying towards 2022, so that it matches the original value after all,  TT won't let me change it back to the higher number--it caps me at the lower refund value.  This doesn't make sense: either I get to apply the original (higher) refund to my 2022 1040-ES and I make a payment for the difference now *OR* I apply only the lower refund amount to my  2022 1040-ES and I owe nothing more right now.  It should be one or the other, not both.  Does anyone know how to fix this?

[fanfare · Accepted solution]

do your own calculation of Estimated Tax.

The best way to pay is to select "Estimated Tax" on the  IRS make a payment page on the IRS website. (more recommended).

Or you can get Form 1040-ES from the IRS website and mail that in with a check. (less recommended)

[BayArea2020]

UPDATE for anyone who encounters this thread in the future... 

I talked to a phone rep who agreed with my interpretation that the ES calculations don't make sense in my case, and she walked me through the steps to override the values in Forms view.  Unfortunately, my attempts to fix things just made the ES numbers look farther away from correct, so clearly there's something else going on--that neither she nor I could figure out--about the way the forms are connected behind the scenes.

I decided that my best course of action would be to essentially start over.  I put back the IRA deduction (to undo all the TT calculations in the amended return), and I deleted the overrides I had made, and then I removed the IRA deduction (again), so that TT would do a fresh calculation on the 1040-X.  It still showed that I owe a payment with my amended return, and from what I've been able to learn about IRS rules, that's the way it is supposed to work.  It's annoying to have to overpay, but I'll sleep better knowing that I won't owe an extra penalty at tax time next year.

As @fanfare points out, it's probably best to ignore the TT estimated tax calculations and just calculate yourself outside of the program.  I'm annoyed that the answer to this glitch is to just DIY -- kind of defeats the purpose of paying for tax software in the first place -- but the great part (for Intuit) is that by the time you figure these things out, they already have your money!  Oh well.