Your wife should file a Part-Year Return to Virginia as MFS, since you didn't live at all in Virginia. You are correct that you may want to mail this in.
I am guessing that if you reported both of your incomes to Michigan (including Virginia) and reported taxes paid to Virginia on your Michigan return, that the Michigan tax on the same amount of income in Virginia is much less, or that you overpaid tax to Virginia.
Be sure you indicated in the the MY INFO section of your Federal return, that your wife 'earned income in another state'.
Click this link for more info on filing in multiple states.
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