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Tax help for military filers
You DO qualify for MSRRA. Section 302(B) of the new tax law says this: "For any taxable year of the marriage, the spouse of a servicemember may elect to use the same residence for purposes of taxation as the servicemember regardless of the date on which the marriage of the spouse and the servicemember occurred."
https://www.congress.gov/bill/115th-congress/senate-bill/2248/text
To obtain a refund of incorrectly withheld Illinois taxes, you must file a non-resident Illinois tax return, showing zero Illinois income.
You should also file Form IL-W-5-NR with your Illinois employer. Here's a link to that form: https://www2.illinois.gov/rev/forms/withholding/Documents/currentyear/il-w-5-nr.pdf
Filing that form will cause your employer to cease withholding Illinois taxes.