After recently creating several AD Sites and moving the domain controllers into the newly created sites I experienced a flood of errors in the event logs of all of my Domain Controllers. They were creating errors referencing DomainDNSZones and ForestDNSZones.
Event Type: Warning
Event Source: NTDS KCC
Event Category: Knowledge Consistency Checker
Event ID: 1801
Time: 10:25:43 AM
User: NT AUTHORITY\ANONYMOUS LOGON
The partition DC=DomainDnsZones,DC=domain,DC=LOCAL should be hosted at site CN=somesite,CN=Sites,CN=Configuration,DC=domain,DC=LOCAL, but has not been instantiated yet. However, the KCC could not find any hosts from which to replicate this partition.
For more information, see Help and Support Center at http://go.microsoft.com/fwlink/events.asp.
The other error was almost identical but contained ForestDNSZones instead. I looked in my DNS and did not see these DNS zones which should exist (DomainDNSZones.domain.local). Although I was receiving errors that AD thought they did exist. I tried the DNS tool to Create Default Application Directory Partitions but it created errors also and would not complete. After several hours of research and reading articles that siad my AD was corrupt I finally found something that referenced using ntdsutil to fix the problem although the documentation was not very good.
I was able to figure out that by using Domain Management in ntdsutil I could delete the NC for ForestDNSZones and DomainDNSZones. Once they were removed from AD I checked all of the Domain Controllers with ntdsutil to verify they did not see the replicas any more. I then used the GUI tool in DNS to Create Default Application Directory Partitions. This completely resolve my issue and all of the errors went away. I was able to create all of the AD Sites again without errors.