In my opinion it seems as if the amnesia potion may wear off. Seeing that they had limited sources, they most likely couldn't perfect it anyway. I just think this because it seems as if as the story goes along, Daniel remembers more (Like remembering the girls dress was blue and being able to reassemble the orb) and also his readiness to kill alexander. I personally wouldn't be so ready to kill him. And he was able to find his back through the castle (depending on which ending of course) and seemed to get back to his life. Do you think it's the fact the potion wears off or that it happened to not destroy these memories and desires?