"Eventually, I deleted the origial 1099-R that TT duplicated and downloaded it again and the problem was "fixed","
such modifications cause issues if you want to AMEND your tax return.
You must unwind back to the original incorrect tax return.
AMEND must start with the return as originally filed.
That may not be possible because, as you state, TurboTax no longer does it incorrectly.
In that case, prepare Form 1040-X manually and mail it.
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Always print a copy of your completed tax return for your records, and review it carefully before e-Filing.
You will need it if you are audited by the IRS, to contact the IRS, or to amend if a TurboTax update changes your return or for any other reason,
AND, to find your AGI next year.
@jmafisher
