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.