If I’m understanding your original question, your son lived in company housing in New York City but worked in New Jersey. Taxes were withheld for both NJ and NY.
If that’s the case, then yes, file a nonresident NY return, reporting $0 NY wages.
You will not be able to e-file a NY return with $0 wages. Mail the return, which is good since your return will not match the W-2. Attach a statement explaining that your son’s employer withheld tax by mistake. A letter from his employer would be helpful.
We suggest sending your return by certified mail with delivery confirmation so you have proof of filing.
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