Relinking identical files is SO COOL!
But even professional rippers can miss those identical files... I remember a Maken X rip by a well known group that was released as non-selfboot, and they even claimed that was impossible to make it selfboot without overburn.
But if you looked up closely, there were many identical files that could be relinked, saving enough space to selfboot it without overburn.
I guess that a good practice is to do a "DIR /OS" to see if there are identical size files... then they can be CRC32 checked to confirm the duplicate.
If only those nasty D2 discs had identical files to relink...

I still have the full 4 gd-roms ripped in my HD waiting for a miracle.