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You can do a multi-install in the middle of a current game. Although it will generally serve you better to have a clean original install, and start modding your clone(s). This is more of an issue if play multiplayer alot, especially online rather than on a LAN. But, it doesn't matter much what order you do it in... if you realy want to, you can in theory:
Clone now.
Uninstall the original (now or sometime down the track), including deleting remnant files in the original folder.
Reinstall BG2 to the same original folder, and patch.
Although there may be unforseen problems depending on your specific setup. Note that this is purely theoretical, and untested.
If you do want to start with a perfectly clean slate, I would recomend that you uninstall BG2 completely. This is because, for various reasons, WeiDU doesn't remove dialogue strings when uninstalling a mod. Also, non-WeiDU mods (especially the less reputed ones, like any not formerly hosted at TeamBG) can't necesarily be relied on to uninstall properly.
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