The easiest solution to this issue may be to print and file your joint Illinois return by mail.
According to this Illinois tax agency webpage:
If you file a joint federal return and one spouse is a full-year Illinois resident while the other is a part-year resident or a nonresident (e.g., military personnel), you may choose to file “married filing separately.” Do not recalculate any items on your federal return. Instead, you must divide each item of income and deduction shown on your joint federal return between your separate Illinois returns following the Allocation Worksheet on Page 17.
If you choose to file a joint Illinois return, you must treat both your spouse and yourself as residents. This election is irrevocable for the tax year.
Illinois does require an ID number for e-filing. You can either print and mail your Illinois joint state return, or you can file a separate return for Illinois, which would require creating a different Federal return from which to generate the separate state return.
If you e-filed your federal using the joint married status, but you want to e-file your state returns separately, only one of you will be able to e-file. The other must paper-file their state return. See this help article for more information.
Follow the step-by-step instructions in this help article if you wish to file a joint Federal return and separate State returns. It recommends transferring the joint Federal return to Desktop if you started it in Online so that you can prepare additional mock Federal returns to match each State scenario without having to pay for multiple products (since Online only provides for one return for Federal and multiple states).
@RLieberman
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