More details.
You have it mounted on a Boltor. Or not?
You write as if you deleted an improvement and try to paste it in the same weapon to delete it. Or I didn't get it 0_0
So, you choose a deleting option where it already stands (simple boltor), but it is not removed from it? Does the upgrade level reset? It's really weird. I have not tried it, but logically, it should be issued back as a separate item.