Doing a playthrough where you use checkpoints to see everything is prone to bugs: just because you can use a checkpoint, doesn't mean it's not worth saving properly as well. Unfortunately I don't have a fix to get you beyond the Titus fight - whenever something like that would happen to me I would reload a save from that set of choices. Then, I'd slowly plug away at finding the 'correct' order of choices, using checkpoints, so I can do as much content as possible while still keeping it possible to advance.
Anyways, it's worth doing, but you might've shot yourself in the foot for that particular save game. Be thorough, be patient, and you can use checkpoints extremely liberally while still making it to the end of the current set of content.