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Since he has got subsidiary protection it shouldn't be a problem to get in touch with his home country's embassy in order to get a new passport. Only fully acknowledged refugees are not allowed to contact them because they would automatically lose their protection status.
Have you tried getting in contact with his competent Ausländerbehörde to ask them whether it's possible to get his passport back? It might be possible to get it back if they don't need it to process his case anymore.