incorrect Src Root Domain Srv entry in registry

I recently came to know that one of my first domain controllers has an incorrect entry in the registry HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\NTDS\Parameters Src Root Domain Srv, listed as an old domain controller removed many years ago. There are many articles that I have found about this key but most of them say to delete it but I was wondering if it was that easy? The 2nd domain has the name of the first controller in that key so it appears to be fine. I am using Windows 2003 with SP2.

I dont understand which registry entry you are talking about?

Incase that machine does not exist, then check the below command to find a new DC for sync:

w32tm /config /syncfromflags:domhier /update

After that you will need to run:
net stop w32time
net start w32time

It must be able to find the PDCEmulator usually, which is the time source in the domain automatically.

I am talking about the registry key under HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\NTDS\Parameters, there is a value named Src Root Domain Srv and it contains the name of a server that doesnt exist as a domain controller now.

Try to ensure that the server was properly removed from AD and that you do not have any DNS records to that map to that old server. Also check at ADSS. You can try to follow the below link and make sure that the server is no longer living in your AD:

http://support.microsoft.com/kb/216498