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Tanjamuse - Aaah right - I think you'll need to extract them from the new format file in Metadata Edit. To get the metadata , select the format and hit the blue button with an 'I', to get the cover click the brown book cover.
You could also use the ebook-meta command line tool ===>>>
http://manual.calibre-ebook.com/cli/ebook-meta.html
But say you replaced EPUB and you have an existing MOBI with the old metadata - then you'll have to create a new MOBI via conversion, save to disk or send to device to get new metadata in it.
BR