I don't know if this could be too dark as a theory to be true (i really hope not) but, this bonney could be a clone. Lets say that the sapphire disease is truly uncurable, so what could vegapunk do to save bonney? He could create an identical and healthy clone that has all of the memories of the original+ an artificial df power and make belive kuma that he has cured her to spare him the pain of losing another dear one. I hope that i'm wrong but this could be possible.