Does it shut down over and over every time you try to go back to emunand? Or only just this one time?
This may be caused by extended memory mode which would usually make the 3DS reboot after you exit a game which requires it. Maybe if you shut down the 3DS while in-game instead of letting it exit Smash and reboot it could cause a never-ending problem with emunand shutting down every time you try to access it since it never actually got to exit from extended memory mode properly. I don't know, just my uninformed view on the matter.
If if does it every single time you try to access emunand, I hope you have a recent emunand backup.