I've done the typical process of data transfer: insert original SD card, copy files onto computer, eject, insert new SD card, copy files onto new. When I first booted up the system with the new SD card everything showed up just fine. I even played a game that I saved on my SD card to see if everything was in tact. However, the next time I turned it on it said that an SD card was not detected.
I then enlisted the help of my boyfriend who said to transfer the files out again, format the card to NTFS, and then transfer them back in. Still nothing. I let him borrow it and he tried to see if it was a problem with the card so he transfered everything to a spare he had. I tried it out and at first everything worked just fine, all the games were back. But when I went to look up something on the eShop channel and then came back to the home menu all the games were gone except the Four Swords Anniversay Edition game (which played fine and retained my save data). The 3DS didn't even say that it didn't detect an SD card, the games were just gone from the menu.
Hopefully there's a solution to this I'm overlooking; I'd really appreciate the help.