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It sounds like you went mucking about in the files maintained by Calibre. That's guaranteed to make a mess because Calibre is only aware of the changes it makes there.
The trick with your Calibre library is to leave it alone. Don't even open it to look inside. Hide it someplace deep in your directory if it offends you. Just leave it alone and let Calibre deal with it.
If you want to extract books from Calibre, Save to Disk will put the desired books wherever you want. Trust the metadata that you see within Calibre. It only gives me duplicate books when I add the same book twice, and then it warns me that that book is already in Calibre. Or were you talking about the same book in different formats?
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