wait... if i remember correctly the guys in revivedc used to use some linux app to relink files. i have never used it b4 though.
i remember comrade and atreyu talking about it, i also think tuxthewise had a way of relinking files too.
i think ppl have said -duplicates-once does not work properly?? idk
maybe you could create a batch file to copy the names of all files in a dir searching all sub directories and folders etc..
search for duplicates, once you know the names of duplicate files.
dummy the duplicates to 0 bytes.
then modify sort.txt each instance the duplicates are listed in sort file you point them to the directory of the non dummied file/s
that might be more work than is needed, but it would produce the same effect.
decreasing size of iso a bit to help fit cd-r, and optimizing load times maybe?