Exchange Server Using Wrong Active Directory Site

Our Exchange 2013 server suddenly started logging errors about bad replication between sites (there should be no replication as there is no other server) as well as several other issues that appear to be related.

We have two sites connected by VPN. This is the Active Directory Sites configuration:
There are multiple subnets at each site and the routing between the subnets and the sites is working fine.

The Exchange server's IP address is 10.10.0.26 and it is running on the same Hyper-V host as a DC with the IP 10.10.0.21 (the one named XXXX-DC01 in the picture) which is set as part of the Default-First-Site.

The Exchange server thinks it is in the YGXXX site:

I enabled NTLOGON.LOG, but the only related information appears to be:

How can I figure out why the server is choosing the wrong site?

The Microsoft article KB247811, How Domain Controllers Are Located in Windows is useful here.

That said, here's a list of things I'd check if you haven't tried them already:

• Run dcdiag.exe on all domain controllers to see if they've been having trouble replicating. You may also want to check the event logs -- sometimes I find them easier to read than the dcdiag output.
• Make sure the XXXX-DC01 server's IP address is listed in the DNS servers listed in your Exchange server's network connection properties. If the YG site DC is listed in there, consider removing it if it provides no meaningful redundancy.

• From your Exchange server, test DNS lookup:

  c:\> nslookup
  Default Server: XXXX-DC01.xxxxxxxxx.edu
  Address: 10.10.0.21
  
  > set q=SRV
  > _ldap._tcp.xxxxxxxxx.edu
  

• If you don't get a response that points to your first site DC, you have a DNS connectivity problem, a DNS server problem, and/or an FSMO problem.
• If you do get a good response, then try running an LDAP query against the DC servers returned as a result. Given your setup, you likely already have Active Directory Users and Computers (dsa.msc) installed on Exchange server. Run that from the Exchange server. Right-click on the root object in the hierarchy and connect to your XXXX-DC01 domain controller. If you can't connect, then you know you have an LDAP problem, either with the service on the DC or with connection and authentication from the Exchange VM.
• If you can connect through dsa.msc, then my last suggestion would be to check FSMOs. This is unlikely to be the problem, but is worth checking. Make sure you have one DC in each site that has a global catalog (the GC property can be changed on the server's NTDS object properties inside Active Directory Sites and Services), and that the schema master FSMO is not a global catalog server. Alternatively, you can just make all the servers global catalog servers. Setting them all is a bit of a brain-dead option, but if you have a small directory structure that rarely updates, it's not the worst thing in the world.