I doubt the HW Clans really learned about the Blakist plans. And if they did, between the WoR and the Jihad, obviously nothing happened so whatever may have been planned by either side never mattered for either side.
Considering the spotty communications between the Sphere and HW Clans, they might not even have heard of the Jihad and what went there, it doesn't help the Jihad was confusing for Spheroids... I can't actually recall if they knew what was going on in the Inner Sphere while the Wars of Reaving happened.
I don't think the Manei Domini/WoB plans of the destruction of all Clans were widely known even in the Inner Sphere. Chandrasekar Kurita did piece things together but i'm not sure how widely this was spread in the end.
As for Manei Domini being somewhere, several (partial?) divisions vanished. What happened to them is unknown.
It is possible they, or more specifically, their descendants are behind the Blackout during the Dark Age but this is pure speculation at the moment.
I would assume the Manei Domini are written out of the story for now, like the Homeworld Clans. Their fate is left open so either players can bring back them for their own stories, or Catalyst can return them should they want to bring them back.