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I also keep my entire library in Calibre, if you add a book that you already have, a warning will pop up that it's either replacing or being added to the book you already have, or a 2nd entry, depending on your settings.
When I got my first ereader I immediately started using Calibre, knowing I'd have to have some way to quickly see if I had a particular book or not or I'd end up with many many duplicate purchases.
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