I agree it is a massive inconsistency. Especially given the short story where Zodiark Spits out primal Elidibus to help reconcile the conflict. Its insuinuated within the story that order has been restored and a long time has passed since the summoning of Zodiark. The issue with the endwalker portrayal is that Amaurot is still a flaming ruin, when there are multiple instances to suggest that life had been restored long enough for the new life to flourish to a level where they could be used to swap out the original sacrificed souls.

my understanding is that the events go something like this:

Final Days begins > Amaurot debate involving themselves > bring samples back to Amaurot to study> Final days reach Amaurot > Zodiark Summoned as last desparate act > Zodiark weaves aetheric shield which stops the final Days > Ancients turn attention to restoration > unknown time passes and life has returned to normal > Ancients still unhappy with loss of those sacrificed to Zodiark > Split appears in populous - some support sacrificing the new life to restore the others, some do not > Elidius withdraws from Zodiark to find reconciliation > Meeting with Hydealyn and her disciples > Hydealyn sunders Etheirys and seals Zodiark away.

There is some things i have assumed in this, based on things we learn from side quests in amaurot. Ultimately though, the depiction of the sundering in Endwalker falls too soon in the timeline. If it is taken as not being a metaphor then the timeline is shortened somewhat :

Final Days > Zodiark Summoned > Zodiark creates shield > Ancients try to sacrifice non ancient lifeforms > Elidibus splits from Zodiark > Hyealyn Sunders.

I think the key issue is we dont know if the lives Hydealyn wanted to save were newly created arcane constructs who later developed souls, or existing people who lived on etheirys outside of the ancients.

The side quests in Amaurot leave it very unclear if the settlements outside of Amaurot are populated by the ancients or different races entirely. If the second route is true (bare in mind both are part conjecture) then the sacrifices are likely other races less magically inclined, which makes sense given the ancients view themselves as "stewards of the star." - this could also be true if there are only ancients though. Which is why i still think the original plot of events is most likely true and Endwalker mucked up the metorphical depiction of the sundering / reconned prior info to make Vanet seem less like a genocidal maniac*. (*Just my view of her actions. not saying she is or isn't.)