Lost DNS

After upgrading to Windows 2008 R2 domain and funtionality levels. New DNS servers running with no issues. Rebooted secondary DNS/Domain Controller, then Primary DNS/Domain Controller (master of operations). Dns won’t load thinking that secondary is the Primary DNS.

Opened secondary DNS, and in deed it was configured as primary. Set it up as Secondary. Primary came up, but after a sometime lost all DNS entries. in both Domain controllers.

Tool DNS of the secondary, and manually entered all DNS on the primary Domain Controller. Working with no problems. But, tried to copy, for backup, the dns flat files from windows\system32\dns location, they are not there!

Any ideas? Thank you in advance.