@largetree Hi.
It seems you just messed up the mame2003 configuration. It should be manageable - even if, worst case scenario, we just delete the right configuration files. :)
It is not related to the EmulationStation controller configuration settings.
So, to confirm:
The controllers work well in other emulators? [Yes?]
Do Players 2, 3 and 4 still retain the ability to move down in the same emulator? [Yes?]
Can you not access that menu via another controller's R2 button, as player 2, 3 or 4? [No?]
Can you not access that menu via player 1's R2 button, and then move as player 2, 3 or 4? [No?]
Did you lose the ability to move in all games in that emulator, or just in one particular game?
Let us know. In particular, the last answer would determine whether we'd need to find the global settings file to delete, or just the rom-specific settings.
In particular, in your <rom folder>/mame2003/cfg , there should be some cfg files. Let us know what are its contents. Exit EmulationStation by pressing F4 (or login to your Pi via SSH) and run the following:
ls -l /home/pi/RetroPie/roms/arcade/mame2003/cfg