What is the best way to avoid this from happening? Its the first time I've had it happen on any of my servers after a mod update.

backup often is what I do. Every two hours i do a backup.

There should be at least 5 previous saves in the FTP for your server, or at least there is for each of mine. Worst case scenario for us is a 1-2 hour rollback, but that's better than losing everything.