I know the problem is there because it happened to me today during upgrade testing. It took me several moments to figure out what had happened to my db. Fortunately, like you I had a backup and could get back to a known state so I could debug it.
Although it would be great if you could confirm it, given the size of your library the test would take ages. Only bother if you have those ages to spend.
Unfortunately the fix requires a change to calibre as well as to CC, so I can't make a new CC release until Friday.