That makes sense. You have to export a save of the game so you have something to replace. The files generated on the old 3DS (like the dat files and export.log files) aren't compatible with the n3DS. So you have to regenerate them on the n3DS. Then you'll be ready to replace the contents of the save folder. That's what I understand from shinyquagsire's post.
lol scared me for a second. SaveDataFiler not working on the n3DS would have been a deal breaker for me as I have Pokemon Alpha Sapphire and many other games I will need to do save swapping on.
Another thing. Does Gateway 3.1 on the n3DS use the new save keys for retail carts while in Gateway mode? I'm curious about that. I don't think it does on the old 3DS.
Here's the problem, it's showing GOOD saves that I just created with the game as corrupted in SavaDataFiler, so I can't even export a blank value to replace the data in
Another thing. Does Gateway 3.1 on the n3DS use the new save keys for retail roms while in Gateway mode? I'm curious about that. I don't think it does on the old 3DS. (classic mode does use the new keys if booted from a sysnand version that supports it and all n3DSes have a version that will use the new save keys)
If not, Gateway will really need to work on fixing the broken save encryption in Gateway mode as it will become a bigger problem on the n3DS when users want to convert their retail games into roms for the gateway card. The saves once extracted from the cartridge will not work because gateway mode does not use the correct encryption.
No, just after restore there is no save data in game (I did it in the past, in the same way on my o3ds and saves were working after restore). Of course I used the same cia for install on n3ds.
You should try making a new game on the N3DS then exporting it, then copying just the save data out of the old folder (from regular 3DS) into the new one and importing it. Don't overwrite the new log file or system files that the N3DS generates in the exported save.