The DNS GUI in Server Admin stopped working, so I deleted everything from /etc/dns and /var/named and I think another directory too assuming Server Admin would regenerate them. Nope. I ran the Server Essentials package from the OS disc, and that made it so I could edit forwarders, but I still can't save any zones through the GUI.
It's a bit of a hassle, but you could always install OS X Server on another Mac (or another partition on your server) and grab the missing folders from there. You might also be able to extract the files directly from the installer packages on the DVD with Pacifist, but I think at least some are created during the initial setup (probably why reinstalling the essentials package didn't do it).