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The content.opf file inside the library book's directory gets updated, but the epub shouldn't.
Were you looking inside the epub with Calibre's Edit book? Because that has an option for 'Update the metadata embedded in the ebook when opening' that you may have turned on.
Searching around, I've found one option in FFF that does update the epub on 'update meta from column':
Under Cover, if you have the 'Inject/Update the cover inside EPUB' option turned on, it will do exactly that, which does update the epub.
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