I think I recall reading its just one byte somewhere in the file, probably in the header I'd guess. Try looking at some locked and unlocked ones in a hex editor and see if you can find a byte thats probably 01 in all locked games and 00 in all unlocked ones.
But I thought cygortool was going to work with locked games?
EDIT: Realized he changed his mind. But yeah, its one byte, probably not THAT hard to find if you have an idea what you're doing. But if you do find out, don't be a jerk. Don't release other people's stuff they've locked as your own, and don't post detailed info on doing it.