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Are all 2000 pages 404's? Do they all have unique URL's? If all 2000 are 404's then Mozbot would pick these up as dupe content as well as 404's but if its only reporting duplicates and not all are 404's then other pages would also be duplicates. 1.) Confirm all duiplicate pages are 404's 2.) Do a scan using xenu link sleuth and see which pages are linking to 404's.