Removing embedded subtitles from Matroska files
Removing "soft" subtitles (where the subtitles are not part of the actual video stream) is a piece of cake when using MKVToolNix. MKVToolNix is a set of tools to create, alter and inspect Matroska files under Linux, other Unices and Windows.
Launch the tool & load your video file. The list of tracks, chapters and tags will be populated. It's then a simple task of unchecking the subtitle(s) you want to remove. Set the output filename, click "Start muxing" and in a few seconds you'll be finished.