What I did was demux the original set and use the original m2v file, so no reencoding it in CCE. (was trying jddobs new ifoupdate method). I changed all the timecodes (subs and chapters) , but when recompiling the audio is out of sync, the subtitles aren't (as far as I can tell), but I don't know if this sync problem has something to do with the video timecode.