From my understanding the used soul is sent to Origenics for cleaning and repackaging while a new soul is activated. Just holding the same soul in might not work as this seems like a rebirth type of thing. The act of getting a new soul might be how they are bringing themselves back from death, so just finding away to hold in the original soul wouldn't work. They also use multiple souls at once for powerups. Without the Endless, they shouldn't run out of souls given they recycle them. The issue they were running into with the Endless was that they were attempting to maintain every person that ever existed for thousands of years, from their medieval age to their cybertech age, that's why some people are dressed like Ye Olden Days while others are dressed cyberpunkish. Not letting a single person on your planet go back into the aetherial sea for thousands of years meant they were constantly pulling from a system without ever putting anything back into it which is how they tapped the well dry on living energy for their shard and was going to move on to other shards.
What doesn't make sense though is Sphene's unwillingness to let us help her. There was likely a way to sustain their memories without the use of soul aether and there was no pressing need to drain the Source RIGHT NOW as the memories could live in the cloud for centuries without fading. She could have always agreed to let us research the matter and get back to attempting to murder the lot of us if and when we couldn't find a solution. Knowing it made no sense that a person with her personality would agree to cooperation first, they threw in another handwave of "oh, the program is controlling her mind and making her act like that." She gave Zoraal's dumb plan 30 years, we can't get three weeks? And why is that program not controlling Cachiua's mind as she stands there and behaves counter to it's every imperative?
No, that's not what happened. The Cahcuia we meet is made up of the Cahcuia memory aether that came from Cahcuia's body and was separated from Cahcuia's soul and grafted onto someone else's soul. The one and only time we hear about any AI is when we're handwaving away Sphene's sudden and ridiculous personality change because it's time for the final dungeon and don't nobody got time for politics anymore. The AI is never mentioned again and we don't see any program doing anything or controlling anything. Also, if these people are data and not memory aether, the absolute need for soul aether makes no sense. We could just run the entire lot of them inside VR and be done. It's only because they are made of memory aether does the need for soul aether make any sense.