Removing old DC from AD, remove "subtree"?
Solution 1:
If you click "View..." in the ADUC MMC and select "Users, Groups, and Computers as Containers..." you will be able to view the sub-objects. If you are running ADUC on an OS newer than 03' I believe that selection is re-named "View objects as Containers...".
Solution 2:
When you say that you had it leave the domain do you mean that you ran DCPROMO on it? It doesn't sound like it. Did you just disconnect it from the network?
I might suggest that you run DCPROMO on the old DC and then delete it, if that's still possible.
If not, and if you've migrated everything (FSMO roles, DNS, DFS, etc.) to the new server then it's perfectly safe to delete the old server. The old DC holds NTFRS subscriptions and that's what the message is pertaining to. You probably have some other manual clean up to do (DNS, metadata) if you didn't properly demote (DCPROMO) the old DC.
Solution 3:
If you want to see all of the objects, you can use Active Directory Explorer. Right-click on the domain, select Search Container, and for Attribute DistinguishedName, select EndsWith, and insert the distinguished name (DN) of your DC, and click Add, then Search.
If you don't know the DN, it is probably something like the following, where DC1 is the DC name, although you may not have DC=domainName, depending on your namespace.
CN=DC1,OU=Domain Controllers,DC=domainName,DC=company,DC=com
At a minimum, the objects are typically:
CN=NTFRS Subscriptions,CN=DC1,OU=Domain Controllers,DC=domainName,DC=company,DC=com
CN=Domain System Volume (SYSVOL share),CN=NTFRS Subscriptions,CN=DC1,OU=Domain Controllers,DC=domainName,DC=company,DC=com
CN=RID Set,CN=DC1,OU=Domain Controllers,DC=domainName,DC=company,DC=com
There may also be settings in the Site Configuration container:
CN=DC1,CN=Servers,CN=,CN=Sites,CN=Configuration,DC=domainName,DC=company,DC=com
So you would want to perform a search for a distinguished name ending with that, or browse that location. There will typically be several settings objects located there, such as NTDS Settings and one or more child connection objects. Even though these objects are not in the same location as the server, they typically have a backlink in the form of the serverReference attribute.
Active Directory Explorer:
http://technet.microsoft.com/en-us/sysinternals/bb963907