You would need to file a nonresident tax return for New York, and make sure to allocate all of your income to Illinois. In other words, show that the amount that you earned in NY was zero. As you answer the questions in the NY return you will get the opportunity to change the amount that transfers over from the federal return to reflect that you didn't earn any of that money by working in NY. See the screenshots below.
If you have questions about this as you go through the NY return, please comment back here.
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