I couldn't find an exact solution to my particular situation so hopefully someone can help. I'll try to be as detailed as I can. Funny enough, trying to replicate the issue I ended up running into an even bigger one so now I think I'm screwed.
I got a 32GB micro SDHC card with an adapter to upgrade from my 3DS' bundled 2GB SD card. I didn't realize the new card I got was only class 4 which gave me some issues and I ended up losing my Animal Crossing (digital, not retail) save and some other things. No big deal, I ended up popping out the 32GB micro SDHC card that was in my phone (also fairly new) which is a class 10, formatted it, formatted my 3DS as well, started using that and seemed to be working for a little bit. Both cards are Kingston.
After a short while my 3DS would give me the same weird error messages when I woke it up from sleep mode after a certain amount time (maybe 5 minutes).
"creating software-management information... please don't remove the SD card."
followed by
"could not create software-management information. there is not enough space on the sd card."
After that, I would shut down the 3DS, turn it back on, and everything would work fine until I put it in sleep mode again and would have to repeat those steps. I was originally posting for help on this issue since I want to use street pass and not have to shut down my 3DS every time I want to take a break from it.
Unfortunately, right now, it won't even recognize my SD card. I put it in my PC and it's now telling me I need to format it. I have an older backup of my 3DS but from what I remember the first time around I did this, the game doesn't allow you to recover older saves and you have to start over. If that's the cae, I'll do it, but my PC won't even format the card. It says it can only format for 8MB on the card (reminder it's 32GB) but even then when I start to format it says.
"Windows was unable to complete the format"
"Check to see that the disk and drive are connected properly, make sure that the disk is not read-only, and then try again."
So I'm a little stuck and don't want to throw out a brand new 32GB card. Any help?
UPDATE!
I started using Disk Management to see what I could to. I ended up ejecting the SD card and putting it back it and it showed the 32GB back with the data in tact. However my 3DS did not recognize the card. I put it back in my PC and it said I needed to format again. Tried ejecting again and putting it back in however this time it did not return the card to it's normal state like before and now I'm kind of upset I didn't back it up at that moment when I had the chance.