No need to apologize, you missed nothing. I never mentioned going from o3DS to n3DS because that was just for the test. I figured if we could CTRNAND Transfer 2.1.0 that it wouldn't be an issue but now I realize that newer firmwares may not work that well. So I have devised a new test. I'll backup my n3DS NAND, movable.sed, ticket.db and title.db, friendsave and other important files, then TinyFormat my n3DS. Then I'll see if I can get it reading my SD card via CTRNAND Transfer and movable.sed import.
EDIT: Alright, experiment over. I managed to restore my system to practically the same as it had been by restoring the following things:
- CTRNAND Transfer
- movable.sed
- seedsave.bin
- LocalFriendCodeSeed_B
- friendsave.bin
My games all appeared on menu and opened, my theme loaded, my friend code, and friend list was intact. The only things that did not restore were my notifications, icon layout (though stored layouts did so getting my icons back to place was easy), Mii's and Mii Plaza Mii's.
I didn't care about the notifications or my icon layout, but the loss of Mii's and Mii Plaza meetings did cause concern, though I believe a save backup from JK's Save Manager will resolve that.
So my backup routine is to dump movable.sed (only needs to be done once), make a CTRNAND Transfer image, dump seedsave.bin, LocalFriendCodeSeed_B (maybe this only needs to be dumped once?), friendsave.bin, and a decrypted save for Mii Plaza and Mii Maker.