Here is the chronology:
1. In March 2021, I made a Roth contribution for tax year 2020 for amount X. I wanted to do a backdoor Roth conversion (contribute to Trad. IRA do a Roth conv.) but alas!
2. Also in March 2021, I correctly did a backdoor Roth conversion for tax year 2021 for the amount Y.
3. While filing 2020 returns, I reported amount X as basis on 2020 Form 8606 (since I assumed I did everything correctly then).
4. 2021 Form 1099-R, Line 1, only shows amount Y, not X Y as I think it should.
How do I correctly file my return for 2021? How do I fix the wrong basis reflected in 2021 form 1099-R? Please help.
You will have to correct the 2020 Form 8606 since you do not have the reported basis and you will have to report the Roth contribution. Please see How do I amend my 2020 return?
If your income is too high you will have to pay the 6% excess contribution penalty for 2020 and 2021. To avoid the 6% penalty for 2022 you can remove the excess contribution with a regular distribution (without earnings or losses) since it is after the 2020 due date.
You can not change the amount on Form 1099-R you only converted amount Y in 2021.
To enter the nondeductible contribution for 2021 to the traditional IRA and report the excess from 2020 on your 2021 tax return:
To enter the 1099-R conversion: