Recently on my 3DS the micro SD card started going bad, and if you never experienced this problem and since there is NOTHING out there about this problem it is something you should know. It began with a newish meaning sealed copy of a DS game Generator Rex. It seemed every time I tried playing this game, I could not load it the normal way with the handheld turned on. I had to load the game while it was off, then turn it on to play the game. I even had to do the same when removing the game, I tried it previously the normal way and it corrupted the save file.
This went on for a few days until the theme I have installed on the 3DS vanished and I started to get “Micro SD Card Cannot Be Found” messages.
I was worried that something was actually wrong with my 3DS as I have never had problems with any SD cards before. I actually called Nintendo and spoke to one of there reps. They thought it might be bad software. It seems they have a downloaded software repair tool for this, but it turns out it took the Rep 15 mins to figure out how to find it.
The results were negative and they suggested it really was the micro sd card. Now for my next big headache copy off the data. Which Windows can do surprisingly as the folders are quite visible. The only problem I had was getting my PC to access those folders. It literally took 9 times, but I was able to copy them off and later install them on a new sd card and I am happy to report I have zero issues with any downloaded software, and all seems to be back to normal.