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.