Try running this from the command prompt ( just replace x with the SD card drive letter):Dear diary, tonight I'm on the verge of a mental breakdown again because of RetroArch on the WiiU. Just when I was nearing the end of the excruciating ordeal setting everything up the way I want it, and while browsing my beautifully constructed massive playlists I suddenly noticed everything disappear. After quitting and restarting, RetroArch would not load anymore. So I powered down the WiiU and put my SD card in my laptop, only to find the entire RetroArch folder being a big garbled mess with corrupted files. Lol, what can you do? ¯\_(ツ)_/¯ Start over, I guess.
chkdsk x: /f
You should definitely also check your SD card with h2testw.