Revisiting some speculation, but something has just occurred to me about Calyx's plan
It's actually quite simple. The chaos he's causing with all the mechanical malfunctions, and attacking people with soldiers is a means to put Everkeep's systems into a state of emergency so he can process his 5000 new Endless en mass.
From Origenics
Information Terminal: All instructions in the processing manual must be strictly observed. As we have charge of the realm's most vital resource, actions resulting in damage or loss constitute a serious crime.
First Stage: Extraction
Mixed aether comprised of both memory and soul is extracted from regulators and transferred into the stabilizing tank. As hastening extraction increases the risk of damage, the rate must not be adjusted except in the event of an emergency.
I think the 5000 number might be Everkeep's upper limit of what can be processed in a short amount of time. However, just because something can be done, doesn't mean it should, and I still think he's not accounting for everyone's emotional state.
"I, for one, have no wish to employ the fruits of my research in this manner. It is a waste of time and effort." After being confronted by Sphene for 'not being fit to be entrusted with the cherished memories of Alexandrians.'
All that soul, and memory aether plus the existential dread of a nation being concentrated into one place is bound to have unforeseen consequences.