That Sudoku app is a DSiWare title. It wasn't deleted alongside the user profile's 1:/data/<ID0> folder because it's installed in the [2:] SYSNAND TWLN.One thing which is weird too, is that, when I restarted the console with the File deleted, and after completing the setup user, on the menu, there was the sudoku app (for the sudokuhax i guess when i did the guide), but I don't get why do i have the game on this console and why on a new user?
Deleting the movable.sed caused as partial factory reset.
Had you instead gone to the System Settings → Other Settings → Format System Memory, that would have permanently erased everything in the Nintendo 3DS folder, the DSiWare games & saves, and the user profile.
Previous 3DS users who did not know about this little but very important tidbit fact were not so fortunate in recovering their stuff.
How's it going on your end with restoring the ctrnand's data and private folders?