I haven't found a good way to handle this yet, but so far I have tried these steps that somewhat help:
-- VSF colour filters: I used 4 colour filters (the Supjav subs use 4 different colours in random sequence). VSF did a pretty good job in creating RGBImages.
-- SubtitleEdit has a feature to combine lines that have similar texts. I tried that feature but the job of cleaning up all the duplicate texts was too much for me

-- I did a visual cleanup to remove the text of subs which are from the same sequence, I kept the last of the sequence untouched. Then I used ctrl-shift-M in SubtitleEdit to combine the empty sub lines with the last sub of the sequence.
-- I did one sub with that method --just posted that in the sub thread. It was very manual and I won't recommend that --may be only for movies that one realy wants/likes;
-- Best option would be if SubtitleEdit could add a new feature: ctrl-shift-M to combine lines that are similar but only keep the last line. That would be the best way I can think of
Let me know if anyone has figured out a working way .