Ok. Another suggestion. Don't put anything on SD (remove SD form console). Make sure your magnet can put your console to sleep and try booting your hacked 3ds. It should boot to Godmode9 but from flashcart. And you shouldn't be able to access SYSNAND CTRNAND.Edit
I flashed it with another 3ds of mine that's hacked. It's an aqua old3ds. The New 3DS XL and Pink are unhacked.
EDIT: Maybe on new Godmode9 they edited it, so that it can access CTRNAND even from flashcart, so I am uploading older one that does not have access for 100% (at least on any console I tried it on)