After checking the streetpass management menu, I closed my 3DS and left it in sleep mode for an hour or so. Returning to it, I back out to the main menu and I noticed that none of the games and applications I downloaded from the eShop are showing up. Checking the management menu, It says there are no games installed, but my extra data is still on the card. I figured I could just redownload my games from the eShop, but it ont let me do that either, mention that my SD is corrupt. That can't be the case, as my streetpass and extra data are still working, as well as pictures and music. I'm afriad of losing my streetpass data, so how do I go about fixing this?
It is possible for some game data on the SD Card to be corrupt while other data is just fine. I suggest that you get another SD Card and use that to redownload your games. You can also redownload directly to the system memory.
Can extra data be moved to another SD card and allowed to work? I don't mind getting a new SD card, but I really want to keep my streetpass data for some games, swapnote, etc.
You could probably try deleting the game data by putting the SD card into a computer and if that doesn't work, just formatting it from the computer. I don't think 3DS supports downloading eShop games to the internal memory (unless they are DSiWare.) This page (click here) has formatting instructions if you try that.
I would try this, but I have no idea which folder would contain game data.
I think there is a Nintendo 3DS folder that would contain the games. I would check to see if it's obvious which folder contains the games.
If you do try a new card, this page (click here) explains how to copy data over.
I tried moving contents of the entire sd to my desktop, but I can only pull my pictures and music from it.
Is there anyway at all to save my extra data?
If you get some kind of error message when you try to copy the games folder, there might be some corruption and it may require formatting the memory card. I would try just deleting the games if you can to see if it will let you do that much. Otherwise I'm not sure there's much you can do.