So you have a .mkv file and want to maybe remove or add subtitles to your video. Back in the way you were out of luck and if you did not have the original files to re-encode again, however now with Matroska it’s a lot simpler. It’s essentially a container.
Using MKVToolNix you can simply open the container, add or remove what you like and then reproduce the container again. No need for codecs, or long rendering times. It’s GUI (graphical utility interface) based, but there are purely command-line methods as well, but I found MKVToolNix to be very simple and gets the job done.
You can download it here. https://mkvtoolnix.download/
Simply scroll down to your preferred operating system (Windows is down below).