I don't know how to do that stuff. I am hack illiterate. It was hard for me putting a seedminer on my system and I still don't understand all the features on the NAND and godmode or what it means to dump your games, etc. Only thing I have used was the QR code for updating and using the freeshop and anemone.
There is a failsafe mode which Ninty uses to fix bricked systems that relies on booting a specially formatted DS mode cart. That combined with the sighax bootrom flaw, which is what makes boot9strap work, means it is possible to modify a DS flash cart to run our own "recovery" software which does not depend on anything on the NAND (built in storage). That is called ntrboot and is something that can't be patched.
Thus, it is possible to back up and restore the NAND data without needing custom firmware or anything. Not only that, but it is quite possible to have a mostly working 3ds system (aside from gba and ds mode software) even if the NAND chip was physically removed.