Amending to combine 2 MFS returns to 1 MFJ return is not easy and the TT program will not do it automatically. The downloaded program is required to make needed changes using the FORMS mode especially for lines 16 & 18.
If you only amended one return then that is correct however I bet you made an error on line 16 or line 18 ... maybe both.
So if you both got refunds on the original returns then the combined refund amount should have been on line 18 ... did line 18 reflect the total ?
Did she have a balance due on her original return ? Did she pay it ? Was this reflected on line 16 of the 1040X ?
