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No problem, and thanks for coming back and explaining the problem. The .af0 files are where the current page number and app settings are stored for each book. If you delete books with the library, then it also deletes the .af0 files, and updates the database. I'm not sure if it deletes the notes, as well, so that's worth testing if you want the notes to continue to exist. Deleting over the USB connection removes the ebook, but leaves the other files around.
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