This is the 2cnd time it happens to me. First time was on the Wood elves with Drycha, as I completed my battle, it prompted autosave and the confederation quest complete (Durthu in this case). I accept it and then I'm just overwhelmed with things to do so I call it a night there.
When I come back, I'm right after the battle, but the confederation prompt is just blanked out, can't click on either options. I can't load previous save either since legendary is only that 1 auto save. Now the same just happened with Rakarth and Karond Kar. The frustration is real... It could be avoided by not blocking the prompts, or auto save when you confederate.