I just fixed this issue on my son's 3DS-XL Purchased in Dec 2014. He said that a message saying the "The SD Card couldn't be recognized. Please end the game and start again." This started happening intermittently and now the card cannot be read.

I noticed that the 4th pin from the lock tab was dirty on the SD card. After cleaning with an eraser still no luck. Tried putting the card into this laptop and there were files on it. I tried a different card in the 3DS and got the same message. Then I snapped some pics of the card connector in the 3DS with my phone to try and get a look at the pins. The contact for 4th pin (clock) was corroded. It looked much lighter yellow than the rest of the pins. I got a micro-SD adapter and cycled it in and out of the 3DS about 15 times. I put the original card and the card was recognized and everything seemed to work.

In summary: If you are stuck with the "SD Card" message try push-in push out another card a lot to try and get to good contact again.