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My understanding is that once he files his return, with the itemized deduction, it should kick up a notice to the wife that her return was corrected and it should lower her to $0 for the deduction. At that point she may have already received her refund, so she would have to return that as well, probably amend her return to itemize (if she can figure that out) and then pay what she would've owed in the first place.

Am I correct?

Yes. IRC 63(c)(6) provides a zero standard deduction if either spouse filing a separate return itemizes.

FWIW, I think he's better off filing separately even if it results in more tax. Does he really want to be tied to her financially for 13 years?

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