Staying on the phone with Nintendo is absolutely my last resort so I was wondering if anyone could help me.

I got the New 3DS right on launch in february and went through with the transfer from my original small 3DS.

However....just a week or two ago when the Mewtwo DLC for Smash bros came out, I attempted to obtain it from the game app itself and the game won't even start because it says it has a problem with the SD card. can't even play the game. I try to boot up fire emblem awakening...says the extra data is corrupted but it lets me play. I try to start Etrian Odyssey Untold....game gives me an error every time at the menu. I try to play Persona Q. It works.......but all my map data is gone. I take a look at the extra data on the SD card.....I see a bunch of slots with question marks in them. It's gotta be those games with the corrupted extra data.

I went months not knowing about this corrupted stuff on my sd card. It had to have been after the transfer because I can't think of anything else that could have done it. I can't delete those question mark slots for extra data. It simply says it cannot be deleted.....does anyone have any idea what I can do to either get rid of this stuff or recover it somehow? any help is appreciated

You could try some recovery software ("Recuva" is a free one). Assuming you have an adapter to plug SD cards into your PC. Probably the first thing to do is to copy the current SD card onto a new one.

I haven't ever done that for 3DS but I don't think it would use a proprietary format or anything (I'm pretty sure I've heard that people just use a PC to copy files over when upgrading to a bigger card, for example). I did have success using recovery software like that recovering corrupted PS3 save files from a USB stick (during move from phat to slim).

EDIT: Good luck!

@quantris: Thank you, I'll try everything you said