This is a bit odd. Did you file one amended return and one new return? How do you know the new return is denied?
What is supposed to happen is this:
1. A and B file MFJ, with A listed first.
2. A amends to MFS. This cancels the joint return.
3. B must file a new original return as MFS, not an amended return. (B can't amend since they never filed an original return that can be amended.)
In this case, if A amended to MFS before the deadline, the MFJ return should be canceled, and B should file an original MFS return. If B files an amended MFS return, that might very well be refused. The answer is to file an original MFS return.
If A's amended return is accepted, I don't see how the IRS can say that B has a valid joint return that can't be amended after the deadline. B can't have a valid joint return unless A also has a valid joint return. Likewise, if B has a valid joint return, how can A amend back to joint when B already has a joint return?
Go over what you filed and read your letters carefully to see what the IRS is really asking for. I suspect there is a misunderstanding at work.
