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With regards to duplicate covers...
I have no idea what would be involved, but finding approximate similarity might be acceptable for images so something like an MD5 checksum comparison might work. The results wouldn't be error free, particularly for a series of books with a rigidly enforced layout/logo, but it would substantially cut down on the number of possible duplicates. Eyeballing a couple thousand covers is not reasonable.
Of course, it also depends on what kind of duplication the OP is looking for. Either multiple books with the same cover image, or multiple cover images within a single ebook.
(Personally this feature would be of no use to me as I explode anthologies and short story collections. I prefer story titles over book titles. So I am going to have multiple books with the same cover.)
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