I really don't know as I do not sync. I just keep what I am currently reading on my reader, and leave my full library on the computer (backed up of course). When I finish a book I delete it from the reader so I never have more that 20 or less on it at once. Good question, perhaps ask in the dedicated Calibre forum here at Mobileread
https://www.mobileread.com/forums/forumdisplay.php?f=166