You will file a Pennsylvania nonresident reciprocal return. Indiana does have a reciprocal agreement with PA. Thus, this return will allow your son to get back all of the PA taxes. It will not be necessary to show zero income to PA, but just IN residency.
In addition, your son may file a form with a PA employer so that Indiana tax is withheld instead of PA tax. Please see the following FAQ on reciprocal states for information on that form: https://ttlc.intuit.com/replies/4776822
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