Bestowing Kakashi with two Mangekyō Sharingan was the doing of the spirit of Obito and not the physical self. So when Kaguya was defeated, Obito’s spirit left Kakashi’s side to join the other world, taking his Sharingan along with him.
Bestowing Kakashi with two Mangekyō Sharingan was the doing of the spirit of Obito and not the physical self. So when Kaguya was defeated, Obito’s spirit left Kakashi’s side to join the other world, taking his Sharingan along with him.