Revelations from Patch 7.2: Seekers of Eternity

[Thighland]

I think you're looking at Preservation (which I did confuse with Oblivion! I blame Bethesda) and Calyx differently than I am, at least. You definitely seem to be looking at him as on some level actively malevolent, someone who would kill an innocent Sphene, more or less, because he can; after all, she's harmless and inert, and merely costs one extra room in the Meso Terminal. That she's useless, and you throw away things that are useless.

I'm looking at Preservation and Calyx as, while essentially antagonistic and evil by story requirement, above all else people with jobs and goals. Calyx has a plan, he has an outlook, and he has steps to achieve, and regardless of whether or not he's all that remains of Preservation or if he's just the head of an unnamed mass, he simply just had nothing to gain from shutting down Sphene's stasis and letting her die. Whether because of plans on the backburner, internal feelings about Real Sphene as the queen, or simply because it's more effort to make a move than it is to not, he just left her there and moved forward with his plans. That even if she is useless, sometimes you don't throw away useless things.

I'm honestly completely ignoring the chance that we'll learn more in the future here, simply because I don't know the future, I'm only speculating on what we have now. And with what we have now it almost boils down to a question of effort: if we accept Calyx's decisions to be the cold logic that he asserts them to be, which is more effort: killing her, or leaving her alive? And is the decision he made truly as driven by logic as he wants it to seem?

You raise a fair point about the possibility that Calyx may not be driven entirely by logic, and I am considering the possibility that he simply doesn't see real Sphene as a threat to his plans. (Although that will probably come back to bite his ass eventually)
Though the interesting thing is that every time something doesn't entirely add up about his plan, it involves Sphene somehow.

Like we can both agree that Calyx' ultimate goal is the key right now, right? Yet in 7.0, instead of looking for it himself, he tasked Endless Sphene to not only retrieve it, but also allowed her full control over it. And either due to being ignorant of or not very loyal to Calyx, Endless Sphene handed us the key personally after her defeat, even though she seemingly didn't have to. Now, if Calyx' goal is to have the key, then why would he leave it in the hands of an autonomous creation whose motivations don't align with his? He basically allowed us to have the key, which doesn't make sense.

Is that something that doesn't need explaining in the future?
It seems to me like Calyx either has an unreasonable obsession with Sphene (and pretends like he doesn't), or there is something special about her, beyond just being the Queen.