As far as canonicity, I don't believe anything has been posted past the Jihad: Final Reckoning book. The prevailing theories, as far as I am aware, are as follows:
1: All the Manei Domini killed off the standard militia for not being true believers, then went mad due to their implants.
2: They have an incredibly well defended, well hidden base on a hidden world, with a multitude of jump ports that they use to restock and gather info from civilization. Some of their super-carriers, with the high-tech jump equipment still survive.
What has been verified, I believe, is that many of the WOBM and higher-level intelligence officers blended back into Comstar and other factions to continue their behind-the-scenes shenanigans. To what end or for what purpose, I don't know.
What I do know is that we will return to bring salvation to the Inner Sphere, and extinction to the Clan heathens. May the light of Blake guide you :)