As mentioned in the user forum... I accidentally hit the key to make a new citebook, and when prompted to save the current one, I chose "yes"... and it overwrote the citebook I was using with an empty file. In other words, it made a new citebook *before* it saved the old one, and then saved the empty one with the old name.
This was not a fluke. I have reproduced this error by making a new citebook with one citation, saving it, making a new citation, selecting "new CiteBook", and saying "yes" to save. Once again it wrote an empty file over the one I was working on.