When you change the metadata or cover for a book using calibre, the book is not updated. The changes are made in the database calibre uses. You have to do something more to get the books updated. Sending the book outside the library using "Send to device" or "Save to disk" will update the copy of the book that is created on the device or disk.
When doing these there are also the "Metadata plugboards". These are ways to fiddle with some of the metadata when the books are sent. A popular plugboard is to add the series name and number to the title of the book as most ereaders have no other way to display this. The plugboards can be created for each format and for each type of device and for "Send to device".
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