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Keep in mind that calibre doesn't embed any metadata unless you take some specific action. Normally, calibre reads the metadata from the book when added to the library and stores this in its own database. All subsequent edits are stored in the database. The data only gets written back into the ebook files(s) when specific action is taken.
Actions that write to the ebook files are the various "polish" functions including plugins, format conversion (data written into the new file but not the original), Save to disk, and Save to device. If you (are foolish enough to) sneak into the library's folder structure to manually copy out a book, that file will not have any of the edited or added metadata unless you've used one of the "polish" functions.
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