Once more the time has come to update my seemingly rather popular guide to upgrading your Nintendo 3DS SD card (previously here). This time, I’m going to cover several scenarios – upgrading your SD (or SDHC) card to another SD (or SDHC) card, upgrading your SD/SDHC card to a 64GB or larger SDXC card, and upgrading your 3DS to a New 3DS, transferring everything to a MicroSD/SDXC. EDITED 11/02/15 to clarify some points in Section 3
Firstly, some information:
Nintendo’s published method for transferring data from SD card to SD card mostly works, but some stuff sometimes doesn’t make the transfer, or does but is inaccessible. For example, sometimes photos are missing, or you lose your play coins or streetpasses. My method (Section 1, below) transfers and retains access to the lot.
Also, Nintendo only officially support SDHC cards of up to 32GB in capacity, but in fact SDXC cards work too. The main incompatibility is not with the cards themselves, but with the partition format SDXC cards use – by default, exFAT, or sometimes NTFS. Neither of these can be read by a 3DS.
Thankfully, 64GB and 128GB SDXC cards can still be formatted to 3DS-usable FAT32 format. Unfortunately, Windows 7 (and 8) has made this difficult to do by not including the option on the standard disk formatting utility.
So, if you want to use a larger than 32GB card, then follow the steps below (in Section 2) carefully before transferring your 3DS data.
In addition, Nintendo also have a guide for migrating all your games, saves, data, software licences and NNID from one 3DS to another. This works fine, but there’s a faster way if you have a lot of data and have a New 3DS which only takes a Micro SD (or Micro SDHC, or Micro SDXC) card rather than a full size one. That’s Section 3, below.