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I have this same issue, and other than being an annoyance it doesn't cause any real issues. Like has been said, download the update and then drag it to the applications folder and replace.
However, a couple times it's deleted my preferences and when I start it up, it acts like a brand new app. And as others have said, I've never had any other application update remotely like this.
Usually updates are a good, fun and exciting thing but with Calibre....I always do update but I make sure I've got time to do it right and deal with any problems that may arise.
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