FFmpeg

I use FFmpeg to remux .mkv video files to .mp4 so that they will play with a broader range of devices without further conversion. All of the movies on my NAS as .mp4 or .m4v files.

Windows Command Prompt

Remux all the .mkv files in a folder, stripping the metadata.

for %i in (*.mkv) do ffmpeg -i "%i" -c:v copy -c:a copy -map_metadata -1 "%~ni.mp4"

Same as above, but converting the audio to AAC

for %i in (*.mkv) do ffmpeg -i "%i" -c:v copy -c:a aac -map_metadata -1 "%~ni.mp4"