With the newer desktop, I believe you can right click on the book and remove it from the desktop application library. That way it will not sync. I run the beta, so I have trouble remembering if it is in your version as well. If you have two of the same books on your reader, you can also remove one, when you are in "Books", not "I'm Reading" directly from the device--no visit to Calibre needed. I believe this is currently WiFi only.
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