Ok, Let me explain a little more:
When you put a SD card on a 3ds system the 3DS OS create a folder for store the data the folder is:
SD:\Nintendo 3DS\1234567890ABCDEF1234567890ABCDEF\FEDCBA0987654321FEDCBA0987654321\
Where the first folder "1234567890ABCDEF1234567890ABCDEF" correspond to the UNIQUE ID of your 3DS system.
and second folder "FEDCBA0987654321FEDCBA0987654321" correspond to the UNIQUE ID of the SD Card
so, if you have a FIRST SD card with the Unique ID FEDCBA0987654321FEDCBA0987654321 and you want to transfer your data to a new SD Card you need to make the next steps:
- Turn off the 3ds.
- Remove the ORIGINAL SD card.
- Insert the NEW SD card and start the system, start the 3DS and wait until all the wizards finish.
- Turn off the system.
- Put the NEW SD card on a PC.
- Open a file browser and look for the recent created folders, by example:
- SD:\Nintendo 3DS\1234567890ABCDEF1234567890ABCDEF\AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\
- Take note of the name of the new folders.
- Insert the ORIGINAL SD card to PC, copy all the contents to a TEMPORAL folder on your PC.
- Insert the NEW SD card to PC copy all the contents from the Temporal folder to the NEW SD but DO NOT COPY the NINTENDO 3DS folder.
On the
NEW SD card, delete all contents of
SD:\Nintendo 3DS\1234567890ABCDEF1234567890ABCDEF\
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\ folder
now Copy the contents of the folder:
C:\
TEMPORAL\Nintendo 3DS\1234567890ABCDEF1234567890ABCDEF\
FEDCBA0987654321FEDCBA0987654321\
To the
NEW SD card on path:
SD:\Nintendo 3DS\1234567890ABCDEF1234567890ABCDEF\
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\
I know, it's a riddle, but Nintendo does that way to avoid you "upgrade" the SD card, moreover, Nintendo doesn't support officially any SD greater to 32GB but all we know they works just fine.
put the NEW card on the 3DS and turn on as usual, all should work fine now.
As I read on the post your actual setup have several folders inside the SD:/Nintendo 3DS folder so if you have several folder with IDs (32 hexadecimal numbers) that means you has been used that SD on different 3DSs. if you have several folders with IDs on SD:\Nintendo 3DS\1234567890ABCDEF1234567890ABCDEF\ (this is a example) mean you copy data from another SD to this SD.
In any case the only combination of data what works on a 3DS system must be on the correct 3DS/SD ID folders combination.