Where is the dns server configuration file located in OS X Server App on OS X El Capitan?
What is the dns server bundled with OS X Server app on OS X El Capitan and where is the configuration file located?

The dns server is a domain name server used for resolving hostnames to IP adresses. The software used are bind. The configuration files for the Server.app are located at /Library/Server/ and the DNS configuration are in a subfolder called "named".

To restore your Server.app functionality, since you haven't configured anything else I would recommend removing the Server.app from your local computer, then remove the /Library/Server folder, and reinstalling the Server.app from the App Store once again.