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AFAIK Calibre either saves the metadata directly in an EPUB's OPF file or saves it in a separate OPF file in the Calibre Library. If Calibre does not updates the tags in the OPF file then Pocketbook of course won't display the tags you changed with Calibre.
So that's why you have to use either the Polish or Embed metadata features. They can be activated from Preferences → Toolbars & menus → Choose a toolbar/menu
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