I'm not sure if I made myself clear before. The disc is set-up in such a way that all the video is in 1 PGC (VTS_02). There are 13 chapters (episodes) that I want to keep, but some of the episodes are followed by supplementary episodes (in additional cells), which are really long and boring, and which play at the end of the episodes, meaning that if I want to watch all the episodes together, I have to keep skipping past the crap bits. If I remove these (not just skip them), I'll be able to fit the resulting DVD onto a single disc without re-compression. But when I rip only the cells (episodes) I want in DVD Decrypter, and burn it to a disc (using VTS_01, all the original IFOs, etc), all but the first episode seem to be lost. It's like it doesn't know where they are on the disc.
I'd like to keep the menus, but change them so they all point to the chapters they're supposed to point to.
I'm sorry if I'm not being very clear, but I'm not clued-up on all the terminology, etc. I'd usually just google for a guide, or check the other guides on Doom9 (thanks for the link, by the way), but I really wouldn't know where to start.