So last night I downloaded a new book and synced my Kobo. After removing the USB and letting the Kobo update I found I had no books listed.
So I re-synced and then kooked at my Kobo in Windows Explorer and Kobo and Calibre and ADE and it all looked fine in all of them.
But still no books on disconnect and update.
Turns out my daughter had 'borrowed' my Kobo and left the book view on the preloaded books, which I had removed. So no books listed.