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If you're just installing the client to fix a game data issue or to a new install, copy the WTF folder directly. Your WeakAuras are saved in that folder. If you want to start your UI over, search the WTF folder for any files called WeakAuras.lua, make a note of what exact folders they appear, copy them, then when you login to your characters again, exit the game and copy those saved files back in to the same spots.
In any case, make a full copy of your WTF folder and just keep that copy somewhere so you always have a backup to go back to if you mess something up. It's always a good idea to occasionally save multiple copies or update a single copy with your current settings.
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