The calibre Library creates its cover.jpg, along with its initial metadata, using the ebook's cover and metadata at the time the book is imported into the library. If you alter the book, with Sigil or calibre's Editor, and alter the cover it will not automatically be reflected in calibre's Library. If you use calibre's Edit Metadata dialog after editing the book, you have the option to select one of the book's formats and set the metadata and/or the cover from the contents of the selected book format. This is done using the appropriate buttons around the list of formats in the Edit Metadata dialog.
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