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You can set how Calibre handles a duplicate book in Preferences, The Add Process tab, check the box for "Automerge added books if they already exist in the Calibre Library" and select your choice from the dropdown menu to the right of that.
I wish a choice was to issue the warning before adding the book, to allow you to check which version of the book is formatted better. But at least you can find the duplicates easily once added and then decide what to do with them if you let it create a new entry for the duplicate book. It will give a message which books were duplicates when finished.
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