In PS2 times was very popular of checking LBA for various of files (some, all, depend of developers phantasy). It is security layer to make life harder for pirates which ripping games from DVD to CD, DVD from videos/music and from DVD9 to DVD5. Maybe Your game is one of those titles.
LBA table can be written in executable, module, module inside IOP image or other resource file.
I writed my previous post simultaneously...
I just guessed it won't works, didn't tried it.
I could try swapping those files and checking if the ISO works. If not then I'd need to find and change the LBA table. Very interesting, thank you for the infos.