Originally Posted by myrroddin
... replace it with the copy from your Desktop, /reloadui, and you should be fixed.
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/reload will trigger WoW to overwrite the files you just copied, WoW also does this on character logout (exiting to where you can select your character). At the point when you're at the character select screen, it's safe to copy the SavedVariable files and WoW will read them when you log back on your character.
There is a way of using
/reload without logging out, but you need to set the files as read-only before doing it and set them back afterward. I've used this method to hotswap macros before, which are written at the same time as SavedVariables.