It can't just happen at random. People with this issue did something unintentionally that screwed the original NAND of the System, but they encountered this problem after they needed to boot the system again, that's the case of the person who said his 3DS ran out of battery and he found this problem. What I mean is that apparently you won't notice this until you exit emuNAND.
Kyogre I can 100% assure you that I haven't done anything out of the ordinary.
just the usual routine... system settings then ds profile.. it froze, and i got ther erro on reboot