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 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.