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When you update the over is Edit Metadata, Calibre is merely updating its stored metadata, and not the actual eBook file.
Calibre will try and update the metadata and cover during a Send to Device operation, but updating the over will only work if it is correctly identified within the ePub file (in many cases it is not).
To ensure a cover update 'sticks' it is often necessary to run a conversion (ePub->ePub will do) as ePub files produced by the Calibre conversion process always correctly identify the cover.
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