I had an issue where a video file had embedded (soft) subtitles with an error, and I wanted to edit the subtitles. Since it's just a stream in the file, it's really easy - at least for an mkv container.

All you need to do is extract the subtitles, edit them in your editor of choice, then add the stream back in. Previously, I removed the subtitle stream from the file entirely then added the edited one back; the updated version simply uses the video and audio from the original file, and the subtitles from the edited srt file, to make the new video output.