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As well as storing the metadata in the Calibre database, Calibre also saves the metadata in a file called metadata.opf with each book. This can be used by Calibre to reconstitute it's database.
As far a getting a cover inserted into an ePub book the easiest way is to run a conversion in Calibre ( even it is ePub -> ePub ). Another easy way is to use the Sigil ePub editor.
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