To begin with, Let us not focus on tangential questions as to "Why would he do it?" and "What would arise out of doing it?" and so on. I would simply like to hear a yes or no answer with a logical argument backing it up.
If one says that God cannot destroy the soul because Bhagwad Gita or some other scripture states soul to be eternal and a part of God then technically God cannot be omnipotent, for it shows that there are things outside his capacity.
If a being is truly omnipotent, He should have the power to change the nature something eternal like the soul into non-eternal as well and subsequently being able to destroy it. So, the question is, is such a thing possible for God?