I’ve managed to change them so retroarch sees my numbered buttons. It still won’t save. When I go into input for user two and click bind default all it changes to how I want it. But it just won’t save!!
I've done some tests recently and it seems the video_threaded = true setting is causing the black video in RetroArch.
If you're willing to give it a try, modify the setting in /opt/retropie/configs/all/retroarch.cfg or through the Advanced configuration editor and
put back gl as video driver
disable the threaded_video setting.
After the configuration is modified, you can test again any libretro ROMs/Games - no restart/reboot required.