My solution has been to make full backups of the discs, join the two m2ts streams with tsmuxer, then multiplex them into an mkv with mkvtoolnix. So far, this has been good enough, but it has some shortcomings.
- Chapter information is lost.
- mkvtoolnix lacks the same support for multiplexing dolby vision data that makemkv has.
- On rare occasions, the audio and video streams won't be the same length, probably due to a mastering error. This results in them being out of sync in the second part of the film after joining. This can be fixed by trimming the last second or two off part one with tsmuxer.
- Things could get hairy if a two-disc movie is ever composed of a complex playlist with many m2ts streams per disc.