[dnanian]

I can't think of anything that could happen while we're copying files that would cause your DNS zones to go missing.

I'd suggest looking in /etc/named.conf and /var/named to see if the data is there as it should be. If so, I'd turn off the BIND daemon, rename your existing folders, and carefully copy the stuff from the backup (with proper ownership, authenticated, etc) in to see if it works...