Seems like it has a CLI. You can figure out how to do this action with a CLI command, then do something like find -name *mkv -exec ... to execute that command for all the files.

Emacs Dired would be my goto here, though it’s cumbersome if you dont know the bindings.

kill-rectangle and multiple-cursors within Dired are immensely useful

Edit: Oh, I just understood you want to mass modify the files themselves. In which case wgrep is useful here within Emacs, for modifying multiple buffers.

It essentially runs a grep command on a directory, collates all the results in a single buffer, lets you modify that buffer for all files, and then save in one go

I’ve been using some ancient java app called jmkvpropedit to do this.