Update: I got around this by creating a new retroarch configfile for snes instead of trying to get the snes.configfile= to stick. The new file is located at:

/recalbox/share/system/configs/retroarch/snes.cfg

It works!

Hey there, I am on an rpi5 with recalbox 9.2.3 pulsar. I am editing my recalbox.conf in order to allow using a custom retroarch configuration file.

(I am editing recalbox.conf so I can override my 8bitdo USB gamepad's button configuration, so they work inside SNES emulator. Otherwise I can't get the button mapping to carry over from emulationstation into the emulator itself.)

I am using this setup for n64, which works great, so I can fix the mappings inside retroarch (I set a custom input key to get into the retroarch menu in my custom retroarch.cfg):
n64.configfile=/recalbox/share/system/configs/retroarch/retroarch-taylor-n64.cfg
n64.core=mupen64plus_next
n64.emulator=libretro

but every time I do the same for snes, like so:
snes.configfile=/recalbox/share/system/configs/retroarch/retroarch-taylor-snes.cfg
snes.emulator=libretro
snes.core=snes9x

... something else overwrites recalbox.conf and comments out the settings. if I reopen recalbox.conf later, it looks like:
;snes.configfile=/recalbox/share/system/configs/retroarch/retroarch-taylor-snes.cfg
;snes.emulator=libretro
;snes.core=snes9x

So even if I get it mapped correctly with my configfile setting, for whatever reason it gets commented out and then it doesn't work the next time I go into the emulator.

Any idea why I can't seem to set these settings for snes?