TurboTax will determine your income earned while in Illinois based upon information entered for your federal return, but it may request that you enter amounts in areas where there is a question as to what income was earned where. Therefore, yes, you may have to enter the amounts for IL again when allocating the income on your state return.
And, if initially Illinois thought your earnings were for a full year, it may make sense that at first a refund was shown, but then changed to tax due when the part-year residency was established for the return.
Here is some more information regarding allocating state income on a part-year resident return: In addition, see the other links included below regarding preparation of part-year resident returns.
https://ttlc.intuit.com/replies/4777389
