I have done that and it hasn’t worked. I added the hash hoping that it would force it. I changed it back to as you mentioned, and just chose any button to see if I could get it to respond. I am also having a similar issue moving the hot key in NEO-GEO so I can add coins…(Included as well…

For NES

#include "/opt/retropie/configs/all/retroarch.cfg"
# All settings made here will override the global settings for the current emulator core
input_remapping_directory = /opt/retropie/configs/nes/
video_shader = /opt/retropie/emulators/retroarch/shader/phosphor.glslp
video_shader_enable = false
video_smooth = false
input_b_btn = "11”
input_a_btn = "12”

For Neo-Geo

#include "/opt/retropie/configs/all/retroarch.cfg"
# All settings made here will override the global settings for the current emulator core
input_remapping_directory = /opt/retropie/configs/fba/
input_enable_hotkey_btn = “17”

Is it possible that I’ve removed something somewhere that is telling Retroarch to ignore these other cfg files?