"Copy Newer", which will "union" the contents of the two drives, overwriting older files with newer ones, etc. But this won't make a "bootable" drive in the vast majority of cases, so I'm not sure what you've done.
Also, it couldn't possibly "duplicate" items, since the same item can't exist twice in the same folder. If things were "duplicated", they were in different locations, and thus it's working as expected.
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--Dave Nanian
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