Yeah we don't really know the logistics of how Zodiark can bring back the dead but that one story about phoenix's creation and a soul wandering into the creation intact has me thinking of two possiblities
Souls cannot be created not even by the Amaurotines but they can be perceived by people with excellent eyes like Hythlodaeus or guided around by someone like Emet-Selch so either
A. Zodiark is like a blender and when the sacrificed person is put into him its ground up turned into energy for him to use this means that the soul and all is gone and He can't bring back the people who gave up their lives or they will be lifeless like what Lakshimi did
or B. Zodiark like Phoenix just holds the souls and aether inside of him like cores and when it's time to replace his energy source with the new lives he would pop his old cores out like batteries and the ancients have their people again.
Like Anonymoose pointed out in his Mogtalk with Sly we also gotta find out why Venat thinks Zodiark is but a "temporary fix" before we can fully assemble this puzzle
