Again, the point of the Rejoining is not to get everyone presently on the shards to become Unsundered again.
The point of the Rejoining is to get the worlds to be Unsundered, so they can sacrifice it again to bring back the people they already lost by being sacrificed to Zodiark. The only people they want to "save" are those who are already gone via Zodiark; everyone else, including the souls currently alive, are merely fodder to bring them back.
This was the entire impetus for the summoning of Hydaelyn, because the dissenters went "no, this is not acceptable, we cannot cling onto our civilization at the cost of everything else".
Loghrif was dead, but according to Mitron (and corroborated by every interaction with the Ascians in FFXIV prior), this is a minor setback, since the particular Convocation soul will eventually be reincarnated.Emet seemed to believe that Mitron and Loghrif were dead. Even if they were aware that Mitron had in fact become Eden, it's debatable as to whether it would have either been possible, or desirable in terms of their plans, to try restoring him.
But Emet-Selch (named specifically by Mitron, but again I suspect Elidibus would also be eligible) didn't even bother, because doing so would mess with the one-track plan he had for Rejoining the First through Light.
Ryne: Emet-Selch -- couldn't he have saved you?
Mitron: Perhaps he could have, if such had been his wish. Far easier, however, to simply find another piece of my fractured soul to replace me. From his perspective, there was no need to intervene and potentially disturb with the balance of aether. And so here I remained.
Gaia: So after you failed, he left you here to rot. Some friend he turned out to be.
Mitron: Thus abandoned, I called out for what seemed like an eternity to the only soul who could save me: you, Gaia.