@mveerman -
1) when your wife originally filed that separate return, did she get a refund? if yes, THAT is what the IRS is asking for - asking for the refund back.. Her entire tax return is wiped out as if it never existed and for that to occur any refund she received has to be returned.
2) I suspect you amended your return from MFS (Separate) to MSJ (joint), so that return reflects the total picture of your family, and resulted in a refund.
But I would hope that the return of the refund in #1, net of the refund you did receive in #2 (from both your original tax return and the amended return), put money in your pocket. if not something is wrong as filing joint is less of a tax burden than filing separately.
is that what happened?
