If you download or add a cover to a 'book' (or change its metadata) it will not be inserted into a format file in the library unless you do something to write a new format file with something like
- polish book (ePUB & AZW3 only)
- modify book (ePub only Plug In)
- conversion,
- send to device,
- save to disk,
If its an ePUB or AZW3 then Polish Book is probably the simplest way, otherwise convert like to like (eg MOBI to MOBI). Send to Device and Save to Disk will NOT update the format file in the Calibre library itself. The Viewer reads the files in the library.
BR