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Every time you make a change to your Library (adding or moving books, for example), the sync feature will think you're changing something that needs sync'd to the Reader. Almost every change will generate a separate sync operation.
I usually make all of my library changes before connecting the Reader. That way I only get one sync after I have my books moved into the categories I want them in.
Hope that helps.
ETA: I'm not a big Calibre fan, though it's something of a sacred cow around here. Use whatever tool works for you.
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