I purchased a brand new 3DS XL last week. Before even opening the unit, I upgraded it to a larger SD card by copying over all of the data from the default card to the new one. The new card is a 16GB SanDisk (Same exact card I have in my own unit. This unit is a gift). I then powered the unit on, set all the settings, created all the accounts, etc. 2 games were downloaded: animal crossing and mario kart 7. The unit worked fine, both games ran without a problem.
The following morning, when the unit was open, an error message appeared on screen. "Could not detect an SD Card. The software on the SD card could not be displayed". We restarted the unit and it seemed to work fine, but then the same error message popped up as soon as we tried to start a game. This happened on-and-off all day. Later in the afternoon, I decided to switch back to the default SD card and see if it was a card issue. The unit worked fine, so I ordered a new SD card.
The unit has been working fine all week and the new SD card came yesterday. I copied over all of the data and powered the unit on. All the games ran fine and it appeared good. Well once again this morning, the same error message appeared on screen and the same issue is repeating itself all over again. It seems to be connected with the new SD cards, but I have no clue what the issue would be.
It looks like Nintendo recommends using the following formatter: https://www.sdcard.org/downloads/formatter_4/
I didn't use a formatted for my own 3DS Xl unit, but I may try this tonight since nothing else seems to be working. Any help would be greatly appreciated.