It's missing the fact that you the player is controling all the clones of the same character at the same time. They move as one unit implying that the entities are controlled by a meta entity containing the character's soul. When you are turning bodies into other characters the soul does not remain, it's control gets passed to the other meta entity that still has one soul despite how many bodies it gets. It's not a body swap scenario, it's a teleportation paradox mixed with the good old theseus ship paradox. If the original atoms composing your bodies have been converted into the body of another but your soul still exist in a vessel created 30 minutes ago to be an exact replica of your original body, are you still the same person?