I fired up Mario Kart 8 tonight and found that the data had all been reset. I checked the storage settings and found that there were two files, one that was 64MB and was named my data and an 84MB file called shared data, which I'm guessing is my old data. I'll contact Nintendo tomorrow to see if they have a solution or are working on a patch, don't think I'll get a useful response but I would like to know from someone that's available before I call, do you have two files like I do or just one personal file? Or does anyone know how to make the shared data the actual data?
Edit: I only have one account/profile on my system and is logged in to by default on system startup.
Did you perhaps login on the wrong account? I know my girlfriend panicked thinking she'd lost all here saves on 3d world as she was under my profile rather than hers. I'll try and check my save data and see what I files I've got, but i think that's what my other games look like.
At least now you have the joy of unlocking it all again, talk about replay value!