@baviaannl __Mupen64Plus __ is a standalone emulator, so it's not getting its settings from RetroArch, you can try lr-mupen64plus (which is a Libretro emulator) and see if it works.
For standalone emulators, just like for libretro emulators, ES will try and generate an input configuration file when you register your input. If you modified it in-game, then you can edit/reset it as described in https://retropie.org.uk/docs/Nintendo-64/
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