After you file

Sorry to bother you again.

I am in the process of amending my return using TurboTax Deluxe edition after reading your replies.

I did exactly as you advised me to do: I clicked on "amend" my return, went to retirement contributions section under Deductions & Credits, entered the $6,000 original contribution, then when TurboTax indicated that I made an excess contribution of $4090, I explained in TurboTax in Part III of Form 1040-X that I made an  excess contribution of $4,090  to my Roth IRA in 2021 by mistake and that I already called my IRA custodian  and  had the excess contribution returned before the tax filing deadline of April 18, 2022 (and that I had a net loss on the contribution so I don't owe any taxes because of no net earnings  and therefore also don't have to adjust my AGI; also explained that the 6% penalty was already withdrawn in the 2021 tax return and that I failed to notice it at time of original filing a few weeks ago and that I am seeking a refund of that 6% penalty tax I paid). 

On Form 1040-X, there were no auto-populated changes in the numbers on line 10 ("other taxes") as a result of the explanation I typed in about the excess contribution and that I already had it refunded to me. So I went to Form 1040- through the "Forms" option and was able to click on the boxes on Line 10, column B and C and right clicked on each box to "override" and then was able to  manually type in the new numbers/changes in line 10, columns B and C.  Then TurboTax was able to do the math automatically and entered the correct refund amount (the 6% penalty tax I paid/had withheld) in line 22. So Form 1040-X is all set and correct.  

And exactly as you said,  Form 1040-X now only shows a change to "Other Taxes" on line 10. 

The issue is with Form 5329 in the amended return. Form 5329 was not removed from my amended file as you had mentioned it would be (and that I would have to print it off and  manually correct), but instead Form 5329 is included n the amended file but had some different numbers in lines 18-25 on Part IV compared to the original Form 5329.  These changes in the numbers were auto-populated by Turbo Tax and I had nothing to do with the new numbers (ie, I did not manually enter anything on Form 5329):

In Part IV of the original Form 5329:

Line 18-22: are zeros or blank

Line 23-24 :have the excess contribution of $4090

Line 25: has the 6% penalty tax amount.

In Part IV of the amended Form 5329 :

Line 18: has $4090 

Lines 19-21, 23: zeros or blank 

Lines 22 and 24: $4090

Line 25: the 6% penalty tax amount

What I feel should be in each line of Form 5329 Part IV: 

Line 18: (Enter your excess contributions from line 16 of your 2020 Form 5329) Since I had no excess contribution from 2020,  I feel this should be a zero/blank? 

Line 19: zero/blank?

Line 20: (2021 distributions from your Roth IRAs)  Should this be $0 b/c the excess contribution refund/distribution was in 2022 not 2021, or do I put  $4090 (the actual excess contribution) or the loss-adjusted amount (~$3900)  if "2021" is referring to the year when excess contribution happened and therefore the year that required the the early withdrawal/distribution?

Line 22: $0 

Line 23 : (Excess contributions for 2021) Since I withdrew the excess contribution for 2021 I feel this should be $0

Line 25: $0

So essentially I feel all lines in Part IV Form 5329 should be blank/zeros in the amended version of Form 5329 (my Option #12)?  (which is essentially what you said in your previous reply, but just wanted to make sure I wasn't missing something since Turbo Tax did not remove the form as you had said they would and instead populated it with different numbers in different lines compared with the original Form 5329.)

The only other way I can see that might make sense would be to print out Form 5329 and in Line 18 manually cross off "2020" and write in "Excess Contributions from Line 24 of your '2021' Form 5329" and enter $4090; in Line 20, cross out "2021 distributions" and write "2022 distributions" and enter $4090; in Line 23, cross out "2021" and write "2022" and enter $0.  These changes would make it clear that I had excess contributions in 2021 but corrected the issue by withdrawing the excess contribution in 2022.   

I should have this issue cleared up once I figure out what to do with Form 5329 (again I am assuming Option 1 is the way to amend Form 5329 as you initially said but just want to be sure) . Thank you again. 

@dmertz