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After you file
> When my 2020 hits their system the carryover data won't match what they have from 2019.
that’s exactly my concern. I have an incorrect excessive HSA contribution on my 2019 return that I need to remove via 1040X. That (incorrect) value would carry over to the 2020 return. I removed it there, so now the 2020 return is correct but inconsistent with the 2019 return until the 1040X has been processed.
It would seem to be an easy consistency check for the IRS computers to carry out. Not sure that it would immediately trigger an full audit or perhaps just an inquiry, but I definitely would like to be in a position where I can tell the IRS that I already (x weeks ago) submitted the 1040X for 2019 to fix the value. Hence my extension for the 2020 return even though I have it ready to go now.