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I keep all my books in Calibre, and I have several thousand. I don't use virtual libraries, they're all in one pot, so to speak. There is a custom column showing which Kindle the book is on, if any, and a column with reading information. If I'm about to buy/download a book and I'm not sure whether I already have it or not, I just search for title or author in my library. Searching is almost instantaneous, regardless of the total number of books in the library.
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