The main issue of Seth being rendered unconscious was not evident to the members of his party, not even those who were clued into the secret of his identity. It was simply because of a misunderstanding of how his abilities worked by those few individuals.
While Seth did have the ability to split his focus between multiple instances, controlling various bodies at the same time, such as speaking with one body while he fights with another, that was simply as far as it went.
He divided his focus, not his mind or rather his consciousness. Even when he slept, it was mainly his body that slept rather than his consciousness, which was often awake for days on end by bouncing between bodies.
Thus, in rendering him unconscious before he was able to separate his consciousness, and soul, from his 'mortal shell' it meant that he was completely unable to control his puppets back in the city.
