Essentially, test it before you pad the files out.did I misunderstand? You're saying if it DOESN'T crash, it might very well actually swap the mods and apply their effects while in-game?
they are 27.6 and 27.2 kb, the mods. Is that close enough, or do they have to match file sizes down to the byte?
If Crash, the game re-loaded the file, meaning you can swap it out mid-game! From there, you can just pad the files to the same size and it should work from there.
If no crash, then the game likely doesn't re-load the file.