What if this exact same issue arises after making zero changes to a retropie that had been working for several months?
I was playing snes roms for an hour or so, plugged in my keyboard to test out Kodi, and all of the sudden an error began popping up "illegal instruction" when attempting to boot/reboot the Pi.
I've run the retropie update scripts, hoping that could solve the issue but it hasn't. Now the "illegal instruction" does not appear, however the Emulation Station splash screen flashes for half a second, and then its back to the initial boot up command line screen.
My filesystem is far from full, so I know that's not an issue.
I've also attempted to remove one console worth of ROMS to see if ES is overloaded in anyway, to no avail. Any help would be tremendously appreciated.