No. The new copy would be a duplicate of the one you already have, complete with GWX and whatever other mods you have installed. MultiSH3 makes it possible to have multiple installs of stock unmodded SH3, from which you can then add mods to each one while keeping a pristine stock version, but you have to start with an unmodded version.
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“Never do anything you can't take back.”
—Rocky Russo
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