To mitigate at this point your client needs to file a nonresident return with WI to get all taxes paid refunded. You client then of course needs to file resident IL returns. Hopefully, the WI refund covers most if not all IL taxes.
While working this, your client, if they haven't already, needs to file forms W4 with the employer to have the correct state withhold taxes. A WT-4 to have WI stop withholding and IL-W-4 to have IL start withholding.
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