'Standard' PDF's have very limited metadata - Authors, Title, Keywords (Tags), Copyright owner and description.
PDF's do not have 'designated covers', so there is nothing to update. Whatever is put at the start of a PDF with a PDF editor, like those from Adobe, Tracker, Nitro etc is 'the apparent cover', but it could equally well be a page of text as it could be an image. 'Embed Metadata' won't update the 'apparent cover'.
What metadata items are you expecting to see in the PDF, and what sort of phone (I'm guessing Android) and what app are you using.
I suspect most PDF phone/tablets apps don't interrogate the PDF for embedded XML data, if your app does then look in the section labelled "http://calibre-ebook.com/xmp-namespace", otherwise look the PDF properties on your desktop in something like Adobe's Acrobat Reader or Tracker's PDF XChange.
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