I don't know why, but my index has disappeared. I will have to rebuild it. There is nothing in the error or crash logs that suggest why it was deleted, but here's a log of the reindexing automatically starting (and stopping).
8463.LogosIndexer.log
Normally this is not too much of a big deal, but in this case it's terminal. That's because I pressed some of those 'Upload my personal book' buttons back in beta 1, and now Logos keeps trying to download them. The problem is that it won't reindex until they're downloaded, and they can't be downloaded 'cause you haven't finished writing the backend.
So I'm stuck without an index [:(]
<edit>Working in offline mode is providing a solution for the time being.</edit>