Since the subsystem was paid for using contract dollars should the PCO provide disposition instructions for the subsystem? Or not because the subsystem is not the actual deliverable?
I can only guess you are discussing the subsystem that was not incorporated into the PRA during production. If yes, then it appears your scenario is covered in DFARS PGI 245.402-71(3).
I'm also guessing the original contract did not include disposition instructions for other CAP or GFP (if provided). So, you may need to add them and DFARS 252.245-7004 (if not in your contract) via modification. Either way, the guidance and procedures at the PGI citation above should provide you the path forward.