TurboTax will prepare your tax return based upon your entries to the questions in the interview section of the program. You are correct that Iowa and Illinois have state reciprocity as explained in this link.
First, for 2024, I would recommend contacting your employer to ensure they have the applicable exemption form on file for you. Since you live in Illinois and work in Iowa, you should have exemption Form 44-016 on file with your employer to ensure they only withhold state taxes for Illinois.
Next, when you amend your return, be sure to report $0 income as being earned in Iowa. You will need to amend both Illinois and Iowa to ensure both states reflect the correct amount of earnings and withholdings. Please follow the steps in this link for more direction on reporting the wages in the correct state.
Please follow the information in this link to prepare your amended return. Please note, you will only need to amend your state returns.
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