Yes, you should get the full amount of the refund. If the Indiana (IN) return is not allowing you to make an adjustment to the income you can follow the steps here to correct the tax return.
When you are in the federal section of your return and on the Form 1099-R screen, make sure your state income amount is zero (Box 16) but leave the withholding amount in Box 14.
The key is to make sure the tax returns are accurately reflected and reported. This will not create any issue for you and it will properly allocate the income and the withholding.
Please update here if you need further assistance.
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