BobKamman
Level 15

Has it been more than 90 days since the Notice of Deficiency was issued?  If not, file a Tax Court petition first and ask questions (or ask for penalty relief) afterwards.  IRS used to lose a lot of these cases for failure to follow the "supervisory approval" requirements for the 20% "understatement of tax" penalty on assessment of more than $5,000 but lately they have figured out how to beat most of those. 

This used to happen a lot back in the Dark Ages, before Service Centers and the Martinsburg "master file" computer.  File one return in Virginia, another in Maryland, and the two were never matched up.  I think even when two returns were filed in the same district, it wasn't always caught.  But you're not getting the whole story here.  She might have filed two returns, but only one refund would have been issued.  She just forgot about not receiving the second one?  And the 3219 wouldn't have been issued until after they had sent her a CP-2000 for that year also.  

If there's state income tax involved, she'll be hearing from them too, when IRS passes along the information.