"Amend and report the 1099-R and that it is a full rollover."

This would be great but without a form 8915-E filed for 2020 declaring that the withdrawal was a disaster withdrawal, the basic facts are that it was an indirect rollover that took two years. Completing 8915-E adds 1/3 to income for 2020.

"If this had been done right the first time, then you would be doing the amendment for 2020 due to the later repayment."

Agreed. But specifically, what would be amended?

If it had been done correctly would you:

Remove form 8915-E and redo the pension payout to show and indirect rollover? This is what I keep asking, what actually gets amended in the return? Mark the return to be amended in Screen 59 in Lacerte and then what? Delete the Form 8915 disaster entries in screen 13 and enter 1/3 of the distribution in the Indirect Rollover entry in screen 13?

"Was the Gross Distribution amount, the repaid amount?"

Yes, $100,000 out in 2020, $100,000 paid back in 2022.

"If so, you treat it as a full rollover: report the 1099-R and the repayment = net is 0."

It is only a valid rollover if it was a disaster rollover since it took two years to pay it back. No timely election was made to have it show up in a single year (2020) therefore the income has to be spread over three years. Payback in 2022 per IRS means no income recognized in 2022, amend 2021 and 2020 to back out the income. There is no option to consider it all handled in 2020 for "the repayment = net is 0.".

"Your taxpayer took advantage of that repayment provision, so even if there would be no early distribution penalty, you need to indicate it is under the disaster provision."

There is only one way that I know if to do this - 2020 Form 8915-E. Are you suggesting another way?

"Unless you are changing something that changes the bottom line of the 1040, there would be no further action as to refund or balance due."

Since there was unreported withholding accompanying the unreported 1099-R, then yes there is a definite change to the bottom line. Full payback of the distribution nets a $10,000 refund.