Nintendo officially only supports memory cards up to 32GB -- no matter whether you're using SD or microSD cards and which 3DS iteration you own.

SDCard_AXI4 SD Card AXI4 IP SD Card Host Controller with an AXI4 interfaced. A quick and simple solution to get an access to FAT file system from Microblaze soft-cpu. Works only in SPI mode, with ...

Safely ejecting SD cards and USB flash drives is standard practice to avoid potential data loss - at least on the surface, that is.

For more, see: Moving 3DS SD Card Data. The New Nintendo 3DS is officially compatible with anything from a 2GB microSD card up to a 32GB microSDHC card, though larger cards can work as well with ...