Dawntrail's Final Zones destroy everything the story has built.

[Granyala]

We also don't know whether they have been erased from existence or just put back on the 'hard drive'. Their memories might still be there they just aren't consuming Aether anymore. Which is a much better situation than draining vast amounts of Aether to make arcane entities which act human.

They are DELETED. The quest made that abundantly clear.
Krile's parents also wanted to be DELETED because they want their knowledge to be gone for good.

There is no restoring these memories.

I understand that in the framing of the story there's just no time at all to find solutions, but it feels that the story hinges on Sphene and the Scions not actually communicating at all ever. During Solution Nine she gets glimpses that we have a ton of knowledge that is beyond her but is never curious to learn the details.

Yeah I too found that very odd. I mean while Energy is a concern, Sphene would have enough time for a few years of research, especially if she'd just put the endless into storage.

Though that isn't the most obvious flaw of the story. The most obvious flaw is the temporal differential. It is arbitrarily introduced and then glossed over completely.

30 years passed in what was for us maybe a week, if at all. That is a factor of 1.564. This is insane! One Hour on the outside of the dome would mean 65 days inside the dome. At most we were in there 2 days, if not less. Tuliyollal would have a had a whopping 2 MINUTES to prepare for the second invasion.

And at the end, Alexandrians still use their regulators, despite knowing that the system is not sustainable. Heck they even derp around with gladiator fights. Dafuq?

So while I like the whole "moral debate", the story has tremendous logic problems and is ... simply put: not well thought through at all.