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If I understand this correctly, you can "Remove All Formats from Selected Files" to get rid of those redundant books created by Calibre.
However, if you've already updated the metadata on your original files, and use Windows Explorer or other way to manage files, why not just "Remove Selected Files (Delete)".
Sorry bout the questions, I'm use to MusicBee & MP3Tag editors and that industry practice with metadata - self contained files. I'm guessing book vendors haven't agreed on standards like music has done with ID3 and such.
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