I think I vaguely recall that Elidibus left Zodiark's body to act separately from him again? I have no idea how this is possible and whether this means he was still a primal (I think they said he still is...?) or whether he became a normal Ascian again which as a consequence left Zodiark heartless.

But I believe the story said some form of separation had taken place before the sundering and Elidibus had joined Emet-Selch and the others to help them/work with them again.