I tried to inject Zelda: the missing link into the Zelda: Collector's Edition disc, but the game didn't recognize the expansion pak, even though it was injected into Majora's Mask, which uses it. I also tried Ocarina of Time, both master quest and the original. None of these seemed to use the expansion pak, even Majora's Mask, which normally requires it.
EDIT: I got the expansion pak to work, but now many of the roms that I tried don't save.