In my experience, which made me quite carefull with card2-games, animal crossing seems not to store it´s save-data (at least not comepletely i guess) inside the rom, but rather also somewhere on the SD-cards private folder.
I figured this out some days ago, when i tried to fiddle as much of my .3ds save over to a new .3dz save as possible
by getting a friends 3ds for moving and local multiplayer and had to put in multiple backups of my SD aswell as multiple different AC-Roms to somewhat get how they work.
I had my old save "corrupted" under several states after restoring the backup BUT (and that´s the interesting part)
also had it working multiple times after restoring both an old SD-Backup AND a AC-Rom that isn´t supposed to have any savedata at all inside, since it was fresh downloaded, the save however got corrupted by solely restarting the game after saving.
...Then i screwed up badly and deleted the one corrupted save that seemed to be my old one without the new keys, not being backed up so it seems, and my save was gone xD
It nontheless made me curious of how the Gateway and/or 3ds further treat the card2-games and how it really stores the saves...
As for card1-saves (i totally got offtopic before because i felt the need to throw it in)
they are still located at the same location and under the same name for both .3ds and .3dz games (one thing the new MT-firm does better i guess), they just aren´t compatible between 3ds/z as the new ones use another encryption then the old ones.
just search for the ID shown on essh as a filename on your internal SD and back it up, then you are good to go.
