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If you send to device or send to folder, I seem to recall that calibre will add the metadata back in. AFAIR, unless you polish or modify epub, the metadata in the ebook is not modified within calibre's library.
As JSWolf says, use calbre's editor or Sigil to manually remove those lines if you need to get that granular. The other option is to modify the plugin yourself since the majority of the plugins and calibre itself were born from the author's desire for a feature.
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