Today I decided to buy the new Yugioh game through the eShop. I selected "download now", and closed my 3ds and set it down. A few hours later, I picked it back up, and was met with an error saying the eShop couldn't read the SD card. I hit okay, and was at the 3ds home screen, and all the icons from my downloaded games are now missing.
I went into data management, and selecting either software or downloadable content gives the error "The SD Card software-management information is corrupted. Reset it now? This will delete all software and save data".
I immediately put my SD card into my computer - from what I can tell, everything is still there. I made a full backup, and then put it back into my 3ds and told it to go ahead and reset it (to see if I could just copy the data back on afterwards and have it work). Trying this gives the error "Failed to reset". I then put in an old 4GB SD card to see if something was wrong with my 3DS, and it worked fine.
I've looked around online and can't find anyone that's had this same problem (some other similar ones, but nothing that worked for them works for me). I can't stand the thought of losing all my saves - My copy of Pokemon X holds all my favorite pokemon I've been training and transfering through the generations all the way back to the original Pokemon Ruby/Sapphire, not to mention all the hours I've put into the Theatrhythm this past week (it's the only thing that's been keeping me sane with my crazy college workload).
Does anyone know of something I can do? Has someone had a similar problem and solved it? Could I somehow trick it by reformating the card, reinstalling everything, creating new saves, and then overwriting those saves with the old ones? If so, how do I do that - the 3DS files just look like a labyrinth of files with gibberish names, and I can't figure out how to do it.
Any help would be greatly appreciated - I'm at a loss here.