The problem with that is adding artifacts back into the pool will also influence what artifacts get dropped by future transmutes. It would create the possibility of something like: horn of plenty -> unstable spellbook -> horn of plenty. In fact, when fairly late in a game the chance for that might be very high.
It's also not possible to guarantee a player won't go back to open a previous crystal chest, especially now with things like the skeleton key.
The alternative is to simply have transmute fail when the game is out of artifacts, which is something I've got the impression players would dislike more.
