Regardless whether you play the game in sysnand or emunand, here are the steps for CIA version of ACNL where by default it has the anti save restore feature:
1. Just create a new town and play it until you can save in that CIA version of ACNL
2. Use savedatafiler to backup the save-game of this new town, then open this new town garden.dat file and copy/write down the first eight bytes content
3. Open the old town garden.dat file that you want to use and overwrite the first eight bytes content with those from the new town
4. Restore back the save-game of that old town using savedatafiler to the CIA version of ACNL
5. Profit
These steps should work for either old or new 3DS.
Just a side note, we could also disable the anti save restore feature by using the debugger of NTR CFW DEX release (the one with break-point and watch-point capability only for the new 3DS). Here are the steps for the US version of the ACNL game after you get that error message:
1. Make sure the wifi is on
2. Start the game and debugger (by pressing button left-arrow while the game starts)
3. The game will pause at entry point then you need to connect the ntrclient PC application to the 3DS by issuing the following command in the ntrclient:
connect('XXX.XXX.XXX.XXX', 5000 + 0xYY)
where XXX.XXX.XXX.XXX is your 3DS IP address and YY is the process ID for the running game (you could find this ID by pressing X and Y buttons together to get the NTR menu at the 3DS bottom screen and check the list of processes, typically the running game process ID would be at the second from the end of the list)
4. Once ntrclient is connected to the running game, run the following commands:
write(0x0043f414, (0x01, 0x10, 0x21, 0xE0), pid=0xYY)
write(0x0043f418, (0x00, 0x00, 0x20, 0xE0), pid=0xYY)
Again YY is the process ID. Basically these two commands replace the following codes that check the secure value (those eight bytes) in the garden.dat with the one stored in NAND:
0043f414: E0 21 10 05 eor r1, r1, r5
0043f418: E0 00 20 06 eor r0, r0, r6
with the following codes:
0043f414: E0 21 10 01 eor r1, r1, r1
0043f418: E0 20 00 00 eor r0, r0, r0
5. Then run command continueprocess() in ntrclient to continue the game, and you will not see the error message anymore, and you will see your town in the background so you could start playing
6. Profit
Another way is to use the restore secure value feature in the savedatafiler. But you need to have this secure value file first for your old town (I know the format in case you want to try). The version of savedatafiler that I use currently is not able to backup secure value file properly in the new 3DS (missing the last 16 bytes), and this is one of the reasons I develop or use the processes above.
Hope this helps.