www.makemkv.com

Some playlists are like that. I think on all my Stuhio Ghibli blurays there is a playlists which goes like 4 hours always repeating one scene.

You said you know the name of the m2ts files with your commentaries. So you can look through the various playlists if there is one with all of the commentaries (if there is any at all)

If I try to export it with MKVToolnix, I get an error:

--- Errors emitted by job 'Multiplexing to file "Commentary.mkv" in directory "\Temp"' ---
The file no. 1 ('\Temp\backup\TRUE ROMANCE\BDMV\STREAM\00003.m2ts') does not contain a track with the ID 2, or that track is not to be copied. Therefore no track can be appended to it. The argument for '--append-to' was invalid.