I just my New Nintendo 3DS XL today and just tranfered every thing from my current Nintendo 3DS XL. After the transfer process was complete all of the game menu item on my main menu were wildly out of order. After I finished sorting them, I noticed that the DSi Ware games were missing, and only the 3DS games were on the menu. I checked the System Settings for them, but it claimed there was no accessible DSi software data on both the System Memory and the microSD Card. I remember that the source 3DS said it was saving the DSi Ware to the microSD Card durring the transfer. I don't want to lose my game data, or the Anniversary Edition Zelda Four Swords game. Please help.
I was already using an 32GB microSD Card in an SD Card converter on my old system, so after the transfer was done I just had to take the miroSD out of the old 3DS and put it in the New 3DS.