Sounds like they used two servers, and the other was probably a backup server, maybe even a db slave, designed to run the entire web app in case the other was down. This probably lead to it being compromised in the same way the main server was.
There are many good solutions mentioned to this problem, whether it be backing up to physical media once a month, or using tarsnap. I feel though that this could have been easily prevented by running a dedicated backup server, instead of one that was probably vulnerable in the same way as the main server was. In my experiences, vandals usually aren't the most brilliant bunch and usually won't go deeper into your others servers unless it's related to the original exploit, or possibly easier. Of course this could have been more than vandalism, maybe a personal vendetta or something.