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I'm not sure if anyone can help me or even where to put this question.  I have about 700 movies on my server and would like to strip all the subtitles from the MKV movie files. 

The reason is that when I play them back, the subtitles are huge and don't appear to behave according to my Kodi or Emby settings.  However, if I use a .srt file, they abide by the settings.  What I've been doing lately is copying them from the server to my PC, then using MKVMerge to remove the subtitles and save them back to the server.  As you can image, that's taking a tremendous amount of time.  I was hoping for a way to leave the movie on the server and just remove the subtitle.  Something quick and easy.

I can then use Emby to download all the .srt files for the movies.

I don't know your setup or settings but one way is to install MKVToolNix then use the Header Editor to change the YES/NO flags for subtitles.

(2021-01-20, 20:52)Spyderturbo007 Wrote: [ -> ]I have about 700 movies on my server and would like to strip all the subtitles from the MKV movie files. 

Try mkvmerge, part of the ffmpeg package.
# remove all subtitles (copy none)
mkvmerge input.mkv --no-subtitles -o output.mkv
You'll have to add the whole read-all-subfolders routine if you want to do everything in one go.