We went over that sort of issue before with the idea of "patching" the FE GBA protos. ROMs do not work that way. Prototypes are different builds with data stored in different locations, and current patching algorithms are not suited for patching a game into it's prototype form.

To put it bluntly, someone tried to make "patches" for the FE protos, but the filesizes were as big as the ROMs themselves, rendering the patches completely pointless.