It looks like the problem is resolved.
For anyone with the same problem: I had accidentally clicked on the macro "2_tests_completed". Doing so seems to remove the /sys/config.g file and the .bak version from the SD card. The Duet will keep running normally after this, until you reboot. After the next reboot, the Duet won't have any config.g file.
The solution was to put the SD card into a computer and restore a backup of /sys/config.g to the SD card that way. Also - removing this macro from the /macros directory to prevent any more mishaps.