Automatically generated site connectors in Active Directory all default to the same site

Greetings,
I have a Single Forest/Single Domain configured with 17 sites. We are currently in 2003 native mode, but are upgrading to 2102R2. The schema has been upgraded and 3 site have been moved to 2012R2 domain controllers.
Each site has one domain controller, most are 2003 but the FSMO roles are on a Windows 2008R2 domain controller in Site1.
Our network is a mesh, but many site have different bandwidth speeds. In this case, Site3 has a 6mb connection to the network.
When I upgraded site3, I couldn't add the renamed replacement server to the domain. The demotion proceeded properly and the objects were removed from sites and services. I found I had problems with duplicate SPNs which were solved by removing the old and
new servers from AD. I still had problems with the new server and found that replication was now broken. We traced it down to to corrupt automatically generated site connectors that all still pointed to the now missing site3 domain controller. I was able to
setup manual replication connectors and then regenerate the automatic connectors, which now pointed to the (in my opinion) proper servers. I only have one manually created site connector to minor site that is not part of the mesh.
This behavior was noticed back in late 2012 when another replication problem occurred during maintenance and was fixed.
This morning I was working on Site4 when I noticed that all the automatically generated site connectors switched back to the new Site3 domain controller.
Can anyone help me determine why the system seems to prefer site3 as a hub. Is there some setting stuck or configured that would make site3 preferential? I want to avoid more down time if site3 has a problem.
Thanks
Derek

Hi Derek,
>>Can anyone help me determine why the system seems to prefer site3 as a hub. Is there some setting stuck or configured that would make site3 preferential?
This should be decided automatically by KCC. The Knowledge Consistency Checker (KCC), a process running on each domain controller, automatically identifies the most efficient replication topology for our network, based on information we provide
about our network in Active Directory Sites and Services.
The KCC runs at specified intervals to adjust the replication topology for changes that occur in Active Directory, such as when new domain controllers are added and new sites are created. The KCC reviews the replication status of existing connections to
determine if any connections are not working. If a connection is not working due to a failed domain controller, the KCC automatically builds temporary connections to other replication partners (if available) to ensure that replication occurs. If all the domain
controllers in a site are unavailable, the KCC automatically creates replication connections between domain controllers from another site.
Regarding Active Directory replication, the following articles can be referred to for more information.
Active Directory Replication Concepts
https://technet.microsoft.com/en-us/library/cc756899(v=ws.10).aspx
Managing replication
https://technet.microsoft.com/en-us/library/cc757117(v=ws.10).aspx
KCC and Topology Generation
https://technet.microsoft.com/en-us/library/cc961781.aspx
Best regards,
Frank Shen
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