I'm in the same boat.

I filed Fed and State for 2021 for a client and then the found out a day ago a 1099 came in.

So I went to the original return and saved it as a slightly new name (basically added X to the filename).

In the new "X" return I added the 1040-X, checked 2021 and began to add the 1099 which populated the 1040-X accordingly and I added text to support this late 1099 that could not have been mailed by 1/31.

Anyway, in HomeBase in the extended columns to the right it's showing in the Amended column, but if I transmit the return it pops up the SSN duplication and I hit "Yes", so it transmits and gets rejected for duplicate SSN.

So now what?