Thank you very much, Floob and patl. Instead of adding the entire text from my saved .cfg file, I just added the lines representing the buttons I needed changed and voilait worked! I can use this knowledge to make sure the settings in the PSX emulator also stay saved, too.
Now all I have to do is find out why some roms work in PIFBA but not in libretro-fba. Probably need a different dump.