A few years ago my wife and I had separated. It was time to file taxes for 2011 so I filed as "married filing separately" as I had no paperwork or information from her for a joint return. Meanwhile for 2011 she did not file at all.

Years later we were back on good terms and for financial reasons we adjusted 2011's year's filing status to "married filing jointly" instead of "married filing separately" using form 1040X. (Since technically we were still married for all of 2011.) THE IRS ACCEPTED THIS adjusted tax return as well as adjusted the refund for 2011 despite her having not originally filed. I kept copies of all this correspondence.

Now it's 2017 and they are withholding a massive tax refund for last year claiming that she never filed taxes for tax year 2011. How is this possible?

We sent back copies of the accepted tax forms we filed jointly along with THEIR OWN CORRESPONDENCE proving they accepted those forms for 2011 and adjusted the numbers for both of us accordingly. But this is info they already have. What else can we do? We sent this return receipt requested and are now waiting...

Technically they are correct in that she never filed a separate return but since they honored a joint return later does it even matter?

Lots of money at stake here. What else can we do?