I've had some thoughts as to why Hydaelyn is light-aspected in the first place. It's been speculated, and with good reason, that Zodiark took on the aspect of darkness because of the effect it has on aether, agitating the elements, allowing for a more rapid recovery of the planet. This is consistent with what Hythlodaeus mentions following his summoning. A common argument is that Hydaelyn has the opposite aspect because of whom she was intended to "check", and it's reasonable as far as it goes... but it really doesn't seem to be a case of one force being superior to the other, in any way. What allowed her to prevail was her ability to enervate. I'm not aware of that being intrinsically linked to the light, and so I think it's reasonable to assume she could just as well have been a Primal of darkness and she'd still be able to do that.
I'm of the belief that her purpose wasn't so much intended to counterbalance Zodiark, as it was to prevent him from reviving the fallen ancients who went into his sacrifice. That may have entailed uprooting/destroying him and substituting him with Hydaelyn. At present, a lot of speculation about Zodiark enslaving the world and demanding more and more sacrifices does not appear to be tenable, and the crux of the disagreement is instead that they did not believe his summoning had permanently resolved the cause of the Final Days. The Convocation disagreed, and so they took it upon themselves to create Hydaelyn to "check" Zodiark.
It's not immediately apparent how checking him would provide a "permanent solution", but if their diagnosis (correct or otherwise) was that creation magicks are the problem, this suggests that their ultimate target wasn't Zodiark but the ancients as a whole and thus why they believed the "new life" should inherit the world, rather than being moved by any emotional preference towards it... he was simply in the way of doing that and would do the opposite by allowing for the restoration of the ancients who went into him. Elidibus
mentions in his monologue at the end of 5.0 that it was intentional that memory of the ancient world and souls would be wiped, so it's hard to see the whole thing as being accidental, as opposed to targeted at the ancients... even if sundering the entire star may have been an accident.
With all that in mind, I wonder if the choice of light in this regard is to still/pacify the aether that is available to the birth of new lifeforms, and thus diminish it and prevent the resurgence of souls like those of the ancients. This would fit with Lahabrea's comments
here, explain why in spite of all the aether being rejoined to the Source, Elidibus's observed the waning of the souls within it, and also fit with Leveva describing the state inside the star as similar in its description to the First. There is still the question of how all this empowers Zodiark without an automatic pipeline feeding it back into him, but it could just be a case of putting all the aether back where it needs to be and ready for his revival. At the least, the thing he mentions, the Rejoinings, should not be weakening the souls on the Source and so something else appears to be at play.
Anyway, on the OP and thus the defector, my suspicion is that they're the answer to the
question the epilogue of 5.0 poses, and they probably vanished in an attempt to get to the root of the Final Days, since the Convocation was determined to resolve the issue through Zodiark's summoning, and events then worsened exponentially, pushing them to go ahead with their plans. The language used by Venat's crew suggests the 14th was still missing in action, and probably too late to present the Convocation with a solution that would remove the need to summon Zodiark, and also to halt the summoning of Hydaelyn for the same reasons. I don't think it is just the Ascians whom they will seek to deter, but both sides in this war... and if the Final Days were the result of some unknown entity's machinations that we've yet to see surface (perhaps sealed away for now, much like the High Seraph), and not just something wrong with creation magic, put an end to that, too.
Still, it's not clear what effects removing Zodiark and Hydaelyn would have - would it undo his rewriting of the laws of reality, or whatever role she plays in the Aetherial Sea? Maybe, but maybe not. They're both interesting cases as they're Primals summoned with an ancient as a vessel within the star itself, so how far the usual rules around tempering, aether consumption etc. apply, is anyone's guess.