You could probably go into G.E.C.K. or FNVEdit and change them to not be quest items, but I assume they're quest items so that you don't lose them when you're stripped of all your inventory during certain quests, i.e. Dead Money.
If you want to put them back for later, as in not use them for a while and put them back where you found them, I'd just say to disable the mod, save, and then re-enable it when you want to use it. Then everything will be back where it started.