I have a rather puzzling problem. Last night, at around 8 PM CDT I turned on my 3DS to check for the new system update. First, though, I started Swapnote because I received a notification that I had a new note. Once Swapnote started, I successfully received a new note from I Fight Dragons about their new 3D video on Nintendo Video. So far so good. Then, once finished, I pressed Home, then "X" to close Swapnote, as I had done a thousand times before. Then, everything went wrong. I received a message that read "Creating Software Management Information". After that, the Home menu came up as usual, except that everything on my Home menu that was saved to the SD Card disappeared. I promptly called Nintendo of America's customer service department for help, and they pretty much told me that there was nothing I could do, especially since the SD Card I was using was not the official one that came with the system.
At this point I was disappointed, but not without hope. Being obsessed with data security, I had copied everything on my SD card to my computer a few months before, so turned my 3DS off, removed the SD card, and placed it in my computer's card reader. I then deleted the "Nintendo 3DS" folder, which according to the backup I had made, had shrunk from 1.04 GB in February to 5 MB after the Swapnote incident minutes earlier. Next, I proceeded to copy the entire "Nintendo 3DS" folder I had created on my computer in February to the 3DS' SD card. After everything finished copying, I unmounted the SD card, removed it from the computer, and placed it back in the 3DS. Then, when I turned the 3DS back on, I saw that most of Home menu icons had returned. So, I went ahead and downloaded the latest system update, installed it, then went to the eShop and proceeded to download the few software titles that hadn't been restored by my backup. After that, I played around a little with the "Create Folder" option on the Home menu, then turned my 3DS off and went to bed. So far, things don't sound to strange, right? Wrong.
The next morning, I woke up, had breakfast, and proceeded to turn on my 3DS and put it to sleep so I could receive any new notifications, as well as my daily SpotPass weapon gem for Kid Icarus: Uprising. After waiting for more than 10 minutes, I opened my 3DS and was surprised to find that nothing had been downloaded via SpotPass. Immediately my mind went into troubleshooting mode. I checked all the 3DS' Parental Controls, opened Kid Icarus: Uprising and made sure SpotPass and StreetPass were enabled, and also checked "StreetPass Management" under "Data Management" in System Settings to make sure all my StreetPass enabled titles were still enabled. They were. So I immediately called NOA's customer service department a second time, and after talking to them for almost 15 minutes, they were just as confused as I was. I thanked them for what little assistance they had given me, and they created an incident report or some such thing about my problem, just in case this turned out to be a more widespread issue.
After hanging up the phone, I continued to ponder over this perplexing situation, and found myself pursuing a hunch. I went back into System Settings, then Data Management, and then tapped "Extra Data". When nothing showed up (The exact message was "No extra data") I began to get an idea as to what my problem was. So, I called NOA's customer service a third time, and they told me that, from what I had told them, my problem didn't seem to be a hardware issue and that they didn't recommend setting up a repair at this point in time. So, I got off the phone, and continued to experiment with my 3DS in an effort to solve this problem. At one point, I opened up Nintendo 3DS Camera, because, while the 3DS SD card was in my computer, I had checkec the "DCIM" folder and was relieved to learn that all my 3D photos and videos were still there. So, like I said, after getting off the phone with NOA for the third time, I played around with my 3DS and opened up Nintendo 3DS Camera. For a few seconds, the system showed that the latest day on which photos had been taken was in mid-January, which had me worried, because I knew I had taken photos after that day. However, a few seconds later, the screen displayed "Updating Software Management Information" and then all of my recent photos appeared in the list.
This most recent development gave me an idea as to what might be the cause of my problems. You see, after playing around for a while, I discovered that all the software titles that I had restored from my computer to my SD card had their save data intact, which should, if I remember correctly, be stored as several smaller-than-10-blocks files in the "Extra Data" section under "Data Management". In fact, all my save data was present, including the Pokedex 3D data I had from two months ago, as well the four Nintendo Video videos that had been stored on the SD card when I backed it up. Despite all this, every time I checked the "Extra Data" section in "Data Management", nothing showed up. Needless to say, this is extremely puzzling. Even more so because when I turned off the 3DS, removed the SD card once more, and mounted in on my computer's desktop, I took a peek inside the "Nintendo 3DS" folder and found at least one, if not more, directories name "extdata" which contained a sizable amount of data. It appears, therefore, that although the the various software titles on my 3DS are able to find and read the Extra Data stored on my SD card (such as Pokedex 3D data and Nintendo Video video clips), the rest of the system doesn't appear to be aware that data exists. If I'm right, that explains why I'm not receiving StreetPass or SpotPass data, because such data is first stored on the SD card as extra data until the next time the program with which it is associated is launched, at which point it is copied to wherever said program stores such data (which would likely be the game card in the case of Kid Icarus: Uprising, and the internal system memory in the case of Mii Plaza, Nintendo 3DS music, and probably Swapnote, too.)
The way the system reacted when I started up the Nintendo 3DS camera application after restoring my SD card leads me to believe that there is a database file somewhere on the SD card that keeps track of what is displayed in the Data Management sections of System Settings, just as it is well known that there is database or index file on the SD card that keeps track of all the photos and videos saved to the SD card with Nintendo 3DS Camera. So, what I would like to know is if anyone knows what might be causing the Extra Data to not appear in Data Management, and if there is a way to force the 3DS to "rebuild" any database or index file that keeps track of such data, which I believe would solve my problem.
Thanks in advance to anyone who can help me with this situation.