This post discuss a recent trend, where Active Directory Replication appears to be fine but one DC only in one (or more) sites begins logging Knowledge Consistency Checker (KCC) Warning and Error events in the Directory Service event log. I included sample events below.
For those not familiar with the KCC, it is a distributed application that runs on every domain controller. The KCC is responsible for creating the connections between domain controllers and collectively forms the replication topology. The KCC uses Active Directory data to determine where (from what source domain controller to what destination domain controller) to create these connections.