we have run into this twice, different reasons, in July, one was a control server failure (our fault) and the other was a server failure (bad batch of SSD on a web server). Adam helped with both cases.... this is the type of thing where you need to open a ticket as soon as it happens.
By the way @Adam thanks for all the help with the lost DNS records, sites that failed migrations, help with the damaged control server, etc. You rock!