Joining Two MKV files.
sudo apt-get install mkvtoolnix mkvtoolnix-gui
Subtitles are preserved and properly concatenated, so are audio and video. Chapters can be edited in the resulting file with mmg.
This procedure creates a properly muxed file.
Any problems should be mentioned in the “log”-window in mmg.
You can even set and name audio and subtitle tracks with the correct language codes and Annotations like “Forced” or “Directors Commentary”.
If you plan to do this repeatedly on different files you better use the command line version mkvmerge ("mkvmerge --help")
mkvmerge -o output.mkv input1.mkv +input2.mkv