Project E will have a top down camera view, so is unlikely to contain any dragon knights. IMO it would be silly to not do anything else with them, though (especially if Dragon Commander does well).
This is what makes me think it will be explained in the story or you meet the DK from Divinity 2 who appears as an NPC. Even if he / she does not do anything other than tell you "I'm currently working on restoring the dragon knights" or something like that.
As for the Patriarch, I wondered why he didn't get involved sooner. He seems to just has a sit on the fence attitude or does not really care as human's life span is just a blink of an eye for him. Maybe we will see more of him in project E prehaps if he feels directly threatened and needs to take sides.
