Revelations from Patch 7.2: Seekers of Eternity

[Thighland]

So while there might be a bit more to this that we don't know yet, there's three answers here that are probably working in tandem right now.

1. At the time she was put in stasis, Endless were still very much an experimental process (see also: Otis). In that context it makes complete sense to keep her in stasis as you perfect the process, so that you can keep going back to the source for every new attempt.

2. They almost definitely were actually planning to cure her sickness. So keeping her in stasis until they found a cure makes complete sense, and then you hit the tragic truth that they never figured it out, and might have stopped trying at some point; it took outsiders to solve it.

3. She is still the queen. Calyx might have his own priorities, but he likely does still have some level of duty, either on paper or internally as a person, to the queen and the crown, and he and likely the rest of Oblivion know she's still alive. Even disregarding the fact that thanks to Living Memory everyone who was in Oblivion was still around in some form until very recently, deciding to pull the plug on her would eat at you, you become 'the person who killed the queen' even if nobody else knows. And when it seems like her stasis chamber requires very little maintenance or power, you never really have to face that question.

So yeah, it makes complete sense to me that the plan started as 'we keep her in stasis for now', and then 'for now' gradually became 'for hundreds of years'.

You give Preservation's other members a lot of credit, even though it is safe to say that Calyx as an individual has been in complete control of Alexandria for hundreds of years. (Control he loaned out to Endless Sphene, for a mere experiment)
If what Simulant Sphene says represents Calyx' opinion of Sphene, he really doesn't think highly of her beyond her ability to control the masses. And he thinks even less of her people, treating them like lab rats. I don't recognize a sense of duty to his queen anywhere.
Could he have simply ignored Sphene's real body being frozen in the middle of the most important structure of "his" Everkeep? Possible, but it doesn't sit right with me.

But as you said, there might be more to this than we know. I just hope the writers don't forget about it.