Immigration holds are placed on people they assume or know are non-citizens. The burden is unfortunately on you to prove that he is a citizen. You can obtain a copy of his naturalization certificate from DHS. You may need a notarized affidavit from him, but all you have to do is mail the form to him and have him notarize it and send it back to you. All jails and prisons provide inmates with notary service. I would recommend having the certificate mailed back to you so that it is not lost.
Another form of proof would be for him to reapply for a new passport. Again, you can prepare the forms for his signature and pay the fee for an expedited processing.
Another form of proof would be for him to reapply for a new passport. Again, you can prepare the forms for his signature and pay the fee for an expedited processing.
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