chapters points missing from .MKV trimmed with AVIdemux

[DaveIsHere]

Hi VideoHelp, Always liked this place and usually got answers I needed, however this time I searched all around and could not find one. I've been making x264 encodes of television seasons to fit 1 season per single-layer DVD. In short, my calculations were a little too good- in one season I exceeded the DVD space by 65536 bytes (!), probably due to sector boundaries. I trimmed the last 40-or-so black frames of one episode with AVIdemux but the resulting .MKV is 1MB smaller and the chapter points are gone. Latest AVIdemux beta (build 6502) has same result. Any idea how I can restore chapter points to the trimmed .MKV? Thanks

[Baldrick]

Have you tried mkvtoolnix? To extract chapters from the original and then add the new mkv.

[DaveIsHere]

Ah, should have gone cmd line :P Thanks! Interestingly, the recommended mkvtoolnix GUI's were not much help with my problem. AVIdemux worked great for trimming the end of a .MKV file.
edit: I also noticed the subtitles disappeared with the chapter markers after trimming. The command line didn't handle subtitles so I reexamined MKVmerge GUI and realized I made mistake of using "Append" instead of "Add" making the program give me an error. Properly used, things were fine. The interesting thing: I was well below the expected size. Perhaps something is suboptimal with subtitle and/or chapter mark handling in Handbrake (what I use for encoding): if I extracted subtitles and chapter marks from the original to file(sub-chap.mkv), muxed the original without subtitles chapters to file(video-audio.mkv), and then muxed file(sub-chap.mkv) and file(video-audio.mkv) the resulting file is noticeably smaller, more than enough for my purpose and without needing to trim the original at all. Thought I'd share my experience.