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.azw3r and .azw3f are not ebooks. They are additional metadata files containing annotations, including bookmarks, highlights, and how far you got in the book.
If the file in calibre is an AZW3R then it isn't a book, the Kindle will usually have all of these plus the AZW3.
According to the log, you have an AZW3 in your library, but suppose it is possible you renamed an AZW3R and added it anyway?
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