KiriKiri game complains about startup.tjs

I've extracted the main .xp3 file from a game, and tried to patch a single line from the script (one that shows up right at the start of the game) to see if I can succesfully re-pack all the files back in and if I can run the game. Besides that line and loslessly optimizing all the .png files (optipng), I haven't done anything to the game.
But there's a certain oddity to the game as it seems to have 3 patch.xp3 files at the root; and the patch2.xp3, parch3.xp3 files contain the same files as in the scenario folder of the main .xp3 file, and most of them are of same size (haven't checked if they have the same content). Could somebody explain me this tangled oddity, and what could I do?