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... To my annoyance I noted that a lot of books had gone from my library too. When I looked on my HDD, the folder was entact and had the cover in but the book was in the recycle bin. So I had to readd the books and then delete the duplicates.
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You could have turned on the option: Preferences|Add/Save|"If books with similar author and title found ..." and Calibre would have automatically sorted and put the books into the existing records without the need to delete or merge anything.