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Hi, someone correct me if my answer in incomplete but you don't need Calibre to backup your books. In order to backup your books, just copy everything in your Kindle documents directory and system/thumbnails directory.
You should still backup your books bought from Amazon even though all your books are automatically stored in Amazon Clouds. Amazon could theoretically remotely delete your books for whatever reason they see fit. Better safe than sorry since it did happened before to other people.
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