Yes , in case of a game with hardcoded LBA addresses you must patch all of them. Well if you move the very last file of the disc then you only need to patch just one address, however if you edit one files which is in the middle of the filetable and you change its size then no offset will match when you rebuild the ISO, even if you follow the correct order.
It sound complicated but in fact it should be simple. We can code a simple editor (after finding the LBA table in the SLxxx fike and the format of it) to edit the files. The editor would scan the game folder and with the use of a pregenerated LBA filelist(Apache can do this for us) we patch the correct values. After patching we can either make the editor more advanced so that it generates the iso by itself, or we can simply generate the new LBA filelist and let CDGEN do the trick.
To find the LBA table in the main ELF file would be tricky. We must get the start offset and size in bytes of the files in the iso dump and then scan for hex values(I reccomend Hex Workshop) . You may find hundreds of results when searching an offset. Keep a list of it. After searching for a couple of offsets you will notice that some adress are after another, or pretty close to each other. Boom , you found the LBA table.
Then you must find the LBA table format.
It can be:
Start offset size end offset
Start offset end offset start offset end offsets
Just some simple examples.
Things get tricky because sometimes the addresses are hashed, or irregular, or you need to revert the bytes. Rarely does it happen that you find the LBA table after a couple of tries.