I managed to do what I asked by doing what sneaker_ger suggested. But it took quite some time and I had to reduce the filesize to less than 1 GB using Sony VEGAS for a reencode that took 95% of the image quality. With help from MKVToolnix and this program:
https://www.videohelp.com/software/B...b/old-versions
Which also needs Java installed. I used to add a positive and negative delay to the subtitle. Then I splitted using MKVToolnix, and appended again when I had to. This idea worked because I only had to do a few edits, but it wouldn't work with more than that.
As for keyframes I managed to do since between scenes I had a few seconds, so I could instruct MKVToolnix to cut 5 seconds before and don't worry when it was actually going to cut. Of course I also had to calculate how much delay I had to add, and check if it was in sync after I reinserted the edited subtitle files (.SUP) into the Matroska again.
The whole thing is now synchronized, from start to finish, with this new subtitle.
Anyway, it's a shame this can't be done the same way I do with SRTs.