To file IT-40PNR, you will want to set up first that your home of residence is Kentucky, and that you did not work in any other states. Even though you physically did work/receive unemployment from Indiana, because of the KY/IN reciprocal agreement, you are considered to have not worked in Indiana for this purpose.
When you get to the Indiana return (and select it if it does not pre-populate for you based on the other information you've entered into the program), you want to make sure the option for Special Nonresident, or Reciprocal Nonresident is selected. This will generate the form you need and you will claim the refund there.
If that produces a diagnostic, you can go back to the beginning of the Indiana Return interview and select the Nonresident Return instead (which is "officially" the IT-PNR form).
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