First, my library is not 1,000 books, but getting close to 20,000. No way would they all fit onto any one device. Besides, library management on Kindles and on the Amazon website is very poor, collections notwithstanding. In Calibre I can tag, sort, group and view my books in any way I want. Whenever I need to find out if I already have a book (which is pretty often), it takes only a couple of seconds in Calibre. And no, Amazon doesn't always let you know you already have it. If the ISBN has changed, it's listed as a new book and you won't get any notification.
Second, I buy my books from several vendors, not only Amazon. That's because prices elsewhere are often lower for my country (we have no Amazon store of our own). Again, without Calibre I'd be lost and would certainly have bought many duplicates.
Third, I want to edit the formatting in all my books to suit my taste.
Fourth, with a huge library it's much easier to load books to my reader from Calibre than it is to download them from Amazon.
I'm sure there are other reasons, but those four are the primary ones coming to mind.
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