Missing Half of Movie

[Selur]

I tried changing decode settings to use ffmpeg

You need to adjust the settings so that Hybrid will use another source filter in the Vapoursynth script. (no clue what you changed)

Also, I don't know if info is useful, but MKVextract only gets to 37% progress when extracting subtitles and then finishes.

Sounds like something is wrong with the file.

If you play back the file in MPC-HC and similar, the file plays through the complete clip without problems, right? (it does not glitch somewhere)

Cu Selur