This happened to my 3DS just this morning... I read a new note I had gotten in Swapnote and then pressed the Home button to exit out of the app. When i got to the home screen, a pop up appeared and said it was "Creating Software-Management Data." I let it do it's thing, but when it was done all my downloaded games (except for a lone DsiWare title) and Extra Data were wiped from the SD Card. I have no idea what would cause this and I'm wondering if this is a bug. Would like to know if anyone else has any info on this problem.