Roms/.3ds or cia
You can fully backup your internal SD card using USB Image Tool by Alexander Beug. You'll get a binary file that's an SD image that includes the emuNAND partition and all your user data. Keep it safe, like you do with your sysNAND backup.
Then I believe you can just regularly backup your Nintendo 3DS folder. If disaster strikes, restore the SD backup then replace the Nintendo 3DS folder with the most recent one. I don't know enough about the folder to advise if you can just backup specific parts of it. Perhaps someone else knows about that.
How is emunand tool incompatible?Turns out emunand tool is incompatible with this situation. So USB Image tool it is.
How is emunand tool incompatible?
Emunand tool backs up the emunand and the rest of the of the folders can be copied. To restore, format a new emunand then inject the old emunand into the new one thus replacing it and copy the folders back. Does the same thing as as an image tool. Either one works just a different process and different archive sizes. The image takes up more space.
Since when? I have been using it on all 3 of my new 3DSs. Backuped up, restored emunands several times.It does not work with new 3ds.
It does not work with new 3ds.