I've suggested this in the middle of a separate discussion of a possible bug, so I've pulled it out as this is actually a new feature request.
It would be great to have a 'Wireless Sync All Books' option which would ensure that the CC library matched the Calibre one. That would mean any new books in Calibre added to CC, any books in CC that aren't on Calibre deleted from CC, any changed books or tags etc brought over to CC.
It's quite complicated to achieve this currently - in fact the only way of doing it securely that I know of is to delete all books in CC then re-import the whole Calibre library.