Having experimented with creating video for Daphne/Hypseus in the past, it's all about frame accuracy and maintaining FPS. So cropping the (it appears) first 157 frames of video, and the appropriate edit to the audio, (you can perhaps use the existing .ogg file as it should match), then it should (in theory) work in Hypseus. Basically look to match the existing MPEG2 video frames, as that IA MPEG2 seems to have been done by someone who figured it out.
There are ffmpeg commands on how to correctly encode the .m2v and .ogg for Daphne and Hypseus on the Hypseus game LUA GitHub pages. So that would be my starting point. But ultimately testing the video files in the game and carefully watching scene changes are the way to be certain.