Another alternative is to use FunscriptToolbox to do it since it’s similar to synchronizing a script to a remastered video.
If you have LongVersion.mp4, LongVersion.funscript and ShortVersion.mp4, you can simply call:
"C:\Tools\FunscriptToolbox\FunscriptToolbox.exe" as.cfs -s LongVersion.funscript -n ShortVersion.mp4
This will create a ShortVersion.funscript synchronized to the shorter video (using the audio channel).
In that case, you might want to open the resulting .funscript in OFS afterward just to clean up the start or end of the scripts.