Talk with the Insurance Company adjustor, not an independent appraiser, not the repair shop, the actual adjustor who is employed by the Insurance company. He, or she, is the actual person who issues payment. He has the authority to control what happens to the parts as his position is the issuer of payment. He is controlled by his companies rules, but most times as long as he has a receipt for the REPLACEMENT part, which means it was actually installed, then he does not object to the OWNER retaining the part.
I always felt if the owner wanted it, then OK. But if the shop attempted to retain the parts I would go by and pick them up, call the owner and assure they didn't want them. If the owner didn't want them, and most don't, then went into the training room for inspection by new hires and eventually destroyed or sent to Copart if enough value was possible to be sold as salvage. I have moved high end parts from repairable bikes to Copart or IAA and had them sold. The Insurance company has the right, as stated in your policy, to attempt to recoup its loss and that includes selling "salvage" items.