It won't recover unless I do something... sometimes just quitting the iPhone app and then toggling enabling backups works, but not always. I had to completely delete and reinstall the app once to get it to work, and had to resync all 45000 images/videos I had.
I have had the server itself fail in strange ways where I had to restart it. I had to do a full fresh install once when it got hopelessly confused and I was getting database errors saying records either existed when they shouldn't or didn't exist when they should.
I think I am a pretty skilled sysadmin for these types of things, having both designed and administered very large distributed systems for two decades now, but maybe I am doing things wrong, but I think there are just some gotchas still with the project.