Illinois is fine. If the Kentucky income is from wages earned in Kentucky, did Kentucky withhold any taxes on any W2s? If not, you do not need to file in KY due to the reciprocal agreement between the states.
If KY withheld taxes then you want to file there to get those payments refunded to you. Also, if KY withheld taxes I recommend going to your employer and completing a new form K-4 to have KY stop withholding so that you don't have to file there anymore.
For this year, though, in your Kentucky interview you will need to get to the residence question and select the Nonresident Reciprocal 740NP-R.
1. Select "State" from the left hand menu
2. Select "Prepare State" at top of page and "Continue"
3. "Continue" Kentucky
4. "Update" General information
5 "Select a different residency"
6. Indicate "nonresident reciprocal state (form 740NPR)
7. Continue with interview
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