OP, this plot point really bothered me as well since it is not well explained. I fought Zoltan Kulle twice just to hear the dialogue again. As far as I can tell, Adria didn't capture the Prime Evils' souls in the black soulstone and then lose it. She "tagged" the demons' souls so that when the soulstone is completed by Zoltan Kulle, the souls would be absorbed into it. How do you tag a demon's soul? I don't know. Where were the souls for the last 20 years? I don't know. It wouldn't have taken much extra effort to really flesh out this piece of plot. I can't imagine why they didn't.