i thought if you had the official nintendo save data tool it would allow you to do a 1 time transfer i believe..? unless if im wrong. i used this when i transferred my retail acnl to my legit eshop purchase one. it takes the save off the cart completely but i have a feeling that with gateway and savedatafiller that you can just back it up and inject it back to the "cart" (rom) but thats just what i suspect.
also thanks for the saves matt
helped a lot once i got savedatafiller installed and working..i lost my save and wanted to get back to where i was so i was able to get all the items i lost and then some without having to use my powersaves to import the items a few at a time lol