Originally Posted by Phanx
WoW doesn't do anything with the *.bak files, and you do not need to back up or restore them. The only issue would be if you were only backing up and restoring the *.bak files and not the *.lua files, but based on the OP's description, I don't think that's what's happening.
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That's what I was referring to, though it might have been unclear
