In my second playthrough, I've been skipping the story. I know that the story changes slightly in the second playthrough, though, so I hope I haven't skipped anything...

So, can I get a list of all of the chapters that have story changes in them, so I don't skip them? Thanks in advance.

Stuff involving Pelleas changes, and thus DB chapters after that are different, and Tibarn's team is different, as well as the final.

You do get to see new info conversations in the final chapter, and the events involving Sephiran and the Black Knight change if you fulfill the conditions to recruit Lehran.