3DS:Moving SD Cards

This guide is for moving to another SD card to be used in the same 3DS, as the data is encrypted per-console. If you intend to transfer your content to a different 3DS, see 3DS:System Transfer.

This page in a nutshell:

If the SD card is above 32GB, it must be formatted first: Formatting an SD card
Don't use the SD card in the 3DS prior to copying data to it, or games and other applications may not appear.
Copy all the files over to the new card.

Transferring your data to a new SD card (for example, if you would like more space) is relatively easy, but there are a few things that you should take note of:

The 3DS can only read SD cards formatted as FAT/FAT32 (not exFAT or NTFS). SD cards 64GB and larger ship as exFAT, so if your card is of that size then you will need to reformat your SD card.
- Formatting your SD card will delete all data on it, so if there is any important data on it, make a backup of it first.
Due to cluster issues, the 3DS runs into weird issues on SD cards 200GB and larger (in particular, custom themes no longer stay applied and GBA VC has screen wraparound issues). Loading time also gets exponentially longer the larger the card is.
SD cards do not currently exist in a 2TB capacity. If you bought a card of such a size, you've been scammed. You should not use the card to save any important data (including 3DS data) due to data integrity concerns.

Assuming you've taken the things above into account, just copy and paste everything from the old SD card onto the new SD card and everything will be transferred.

Troubleshooting

There are a few reasons as to why this may happen:

The SD card is not being read; try reinserting the SD card and ensuring that there is no dust or moisture
The SD card is not formatted as FAT32
You have used this SD card in this 3DS before and it created a new data folder to avoid accidental data merging

In the final case, navigate to Nintendo 3DS -> (32-character-ID / ID0). If you have multiple 32-character IDs inside of this folder, delete the smaller one of the two.

Your SD card isn't being read and/or you don't have boot.firm on internal memory for some reason. Ensure your SD card is formatted as FAT32 and that there is no dust or moisture in the slot. If all else fails, you may want to check your SD card for errors.