If you're storing important data—such as DNS data—in application partitions, the ability to quickly recover that data in the event of a disaster is crucial. DNS is essential to the function of AD, so the loss of DNS data can result in widespread outages. Therefore, including application partitions such as the DomainDnsZones and ForestDnsZones naming contexts in your delayed-replication scope is a good idea.
You can use Ntdsutil's domain-management functionality to add a naming context to the replication scope of your delayed-replication DCs. The syntax is
add nc replica %s1 %s2
where %s1 is the DN of the naming context you want to add to the DC's replication scope and %s2 is the DC's fully qualified domain name (FQDN). Allow at least one or two replication intervals to pass, then ensure that the DC has replicated in the newly added application partition. To do so, simply run the Microsoft Support Tools command Repadmin /showrepl on the DC. You should see that the new application partition has replicated successfully, as well as the time of replication in the command output. The Microsoft article "HOW TO: Manage the Application Directory Partition and Replicas in Windows Server 2003" (http://support.microsoft.com/?kbid=322669) explains the process in detail. After you add these partitions to the DC's replication scope, the DC will replicate on the same delayed schedule as the domain naming context.