Kovid - many thanks for your response. That certainly fixes the issue of the Kindle copy and the Calibre copy showing as sync-ed. However, it leaves the Kindle Cloud showing the book in question as being available for download, i.e. not on the device. Which is wrong, and messes up my back-up workflow.
I have only tried with two books, but this seems to be a change from the way the Kindle Touch worked. It is certainly different from the Kindle K.