You said "Earlier this year, she made a payment so we don't owe anything and she submitted an extension."
There is no penalty for being late if money is not owed. Trying to file a MFS (Married Filing Separately) return ahead of a MFJ return risks complications.
Q. Can my married separate be cancelled when she files married jointly?
A. Simple answer: no. Tax returns cannot be cancelled, they can only be amended. In your situation, the timing, in addition to the normal problems of switching form MFS to MFJ makes it particularly messy. The fact that an MFJ extension was filed also complicates it. Your other post indicated you may be claiming an education credit. MFS is not allowed to claim the tuition credits.
