Let me guess, you updated your emuNAND to the most recent version? Unfortunately, the most recent update breaks compatibility with 3DS flashcarts. Gateway says they're working on it, but who knows if/when they'll have a fix for it.
So is it safe to just format the emunand through the gateway menu and go back? I have a fuzzy understanding of how all of this actually works lol, don't want to do anything too detrimental (though I did just buy the 3ds XL at wally world and their return policy is quite forgiving ;-), also they had several older models with 12 or lower serial #s was shocked by that, guess 3ds's aren't too popular in my area).