As far as I know the Character items cannot be defused into Bond crystals in the Crafting system (later on that is when the Bond Crystals are introduced).
The reason the function to rerun and reclaim the item is in case you accidentaly sold it, or used it as upgrade material, in the Pre-Personal Equipment slot times, when many of the bumper mechanics that stop you from doing so were not in place. There is no real value in re-running those maps and collecting multiples... Unless of course you wanna run Dupe of the girl and have it equipped on her as well.