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To fill this in a bit - by using Save to Disk, Calibre creates an .opf file (assuming you haven't turned it off). That file has all the normal metadata (custom metadata is not in there, at least it wasn't yet when I last checked - but will be eventually).
When you use Add Books with Calibre, the first thing it does is check to see if there is an .opf file in the folder with your new book, and if there is, it reads that file and uses the metadata therein.
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