I just had this happen to me recently.
All of a sudden, like a week ago, all my settings reset on 3 of my 5 toons.
It was like they had never logged in before.
I had to redo all addon settings, keybinds and ui settings.
Basically everything except macros, which are stored on the server.
Extremely annoying.
It never occurred to me to backup my WTF folder, but I guess I should now.