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Take a look at the library that I attached to my message.
When you run the 'Library Maintenance->Check Library' you get the message "Found no errors in your calibre library database. ..." When I checked 'Yes,' I got the message "The files in your library match the information in the database."
After reading theduck's post, I re-ran things and got an error in the second phase about the author being incorrect, and after deleting the only thing that I could check, it again states that there are no errors in the first phase, and the second phase states that the information matches.
The second book, "Example of a Bad Book Directory" is still present, and does not contain a document file, only the metadata and cover.jpg.
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