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EPUB is the 'package'.
If you use the editor supplied with Calibre, the work is done.
Save to Disk is an EXPORT of the CALIBRE Library 'view' about the book (the format, OPF is the Metadata you see in Calibre, The cover you see in Calibre)
IT may be different than what is in the book INSIDE the Library unless you take extra steps (AKA Polish, embed Metadata or Modify EPUB)
Send to device does the update to the Transferred copy on the fly
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