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Okay, I think the problem might be that visual boy doesn't read your rom hack because I tested the fire red file first, and it worked, then I patched it and it didn't work.
Okay, so I'm using the apply patch to an existing file option. I put the ups file in the first slot and then I put my GBA file of Fire Red in the Second slot. When I precede to click patch it says Failed! Input file is invalid. If this is an error I my part please let me know.