The actual Margin Crusade, led by Confessor Corvinius, perished beyond the spinward front of the Calixis Sector, somewhere beyond Kalf.

I can't help but think Duke Severus might have known about this, maybe even profited by the Imperium's loss. Perhaps a few of the margin crusade's ships ended up in Dominate hands?

No evidence as far as I know, but it would make sense. Duke Severus is a connected sub-sector lord and has ties to old Rogue Trader money, with ties to the Dark Eldar. He certainly stole a bunch of good stuff (Lycurgos Star Fort comes to mind). Throne, he was probably skimming men and gear from the top of the Margin Crusades levies for years.

Makes sense. I can imagine a worn-out crusade officer jumping at the chance of "disappearing" to a job away from any frontline.

Whatever makes lord Severus more guilty serves my plot.