So I have two files of the same movie.
File1.mkv (10GB, english audio but danish subtitles)
File2.mkv (6GB, english audio and english subtitles)

The problem with File2 is that the subtitle is for the entire movie. What I want is just subtitles for the foreign language parts and not for the english speaking scenes. So my goal is to:
1) Create a subtitle file with subtitles ONLY for the foreign language part from File2.mkv
2) Hardcode that into File1.mkv so when playing the playing the subtitles show by default during the foreign language scenes
3) Then make a subtitle file with subtitles for the rest of the movie (all the english speaking parts) from File2.mkv
4) Embed that subtitle file into File1.mkv so that I can turn the subtitles on and off when playing to show subtitles for the rest of the movie

I installed a nightly version of handbrake (don't know what that means, but was instructed to do so from some forum) and had the following settings:


I was hoping this would produce an MKV file from File2.mkv but now it only has subtitles during the foreign language scenes. Then I could use something like MKVExtractGUI2 to remove that subtitle from File2.mkv and put it into File1.mkv. However after all that time spent for handbrake to finish, it didn't work. Any ideas on how to do step 1? Or the entire process for that matter? Thanks