You can test if this is the problem before wiping the emunand, since it was a bit of a pain. Luma3DS
has a bug that can continue to detect a deleted emunand, and I had to manually wipe some sectors of the SD to work around it.) To verify this is what is the trouble, do this:
Boot the 3DS while holding SELECT to get to the Luma3DS settings menu, ensure at a minimum you have selected Autoboot SysNAND.
If you're not sure which emu or sysNAND you're in, you can enable the luma option to show current NAND in system settings and then verify you can get to both emu and sysnand. I'd recommend doing this just to be safe.
Power off and reboot with L held down to get to emuNAND
Install TinyFormat, then use it to format the emunand.
Here's a QR for the latest version...
That will "unlink" the sysnand and emunand again, and hopefully will stop your problem from occurring. You can go through the trouble of removing the emunand afterward if that's what was causing your trouble.