I have tried to do the metadata cleanup that MS recommends to remove the orphan domain. Here is what I did. I changed the names of my server and domains so I hope it's not too confusing to figure out. Thanks for you help.
C:\>ntdsutil
ntdsutil: metadata cleanup
metadata cleanup: connections
server connections: connect to server SERVER1
Binding to SERVER1 ...
Connected to SERVER1 using credentials of locally logged on user
server connections: quit
metadata cleanup: select operation target
select operation target: list domains
Found 2 domain(s)
0 - DC=GOODDOMAIN,DC=LOCAL
1 - DC=ORPHANDOMAIN,DC=LOCAL
select operation target: select domain 1
No current site
Domain - DC=ORPHANDOMAIN,DC=LOCAL
No current server
No current Naming Context
select operation target: list site
Found 1 site(s)
0 - CN=Default-First-Site-Name,CN=Sites,CN=Configuration,DC=GOODDOMAIN,DC=LOCAL
select operation target: list sites
Found 1 site(s)
0 - CN=Default-First-Site-Name,CN=Sites,CN=Configuration,DC=GOODDOMAIN,DC=LOCAL
select operation target: select site 1
Selection out of range
select operation target: select site 1
Selection out of range
select operation target: list servers in site
No current site
No current site
Domain - DC=ORPHANDOMAIN,DC=LOCAL
No current server
No current Naming Context
select operation target: select server 1
No active server list
select operation target: quit
C:\>ntdsutil
ntdsutil: metadata cleanup
metadata cleanup: connections
server connections: connect to server SERVER1
Binding to SERVER1 ...
Connected to SERVER1 using credentials of locally logged on user
server connections: quit
metadata cleanup: select operation target
select operation target: list domains
Found 2 domain(s)
0 - DC=GOODDOMAIN,DC=LOCAL
1 - DC=ORPHANDOMAIN,DC=LOCAL
select operation target: select domain 1
No current site
Domain - DC=ORPHANDOMAIN,DC=LOCAL
No current server
No current Naming Context
select operation target: list site
Found 1 site(s)
0 - CN=Default-First-Site-Name,CN=Sites,CN=Configuration,DC=GOODDOMAIN,DC=LOCAL
select operation target: list sites
Found 1 site(s)
0 - CN=Default-First-Site-Name,CN=Sites,CN=Configuration,DC=GOODDOMAIN,DC=LOCAL
select operation target: select site 1
Selection out of range
select operation target: select site 1
Selection out of range
select operation target: list servers in site
No current site
No current site
Domain - DC=ORPHANDOMAIN,DC=LOCAL
No current server
No current Naming Context
select operation target: select server 1
No active server list
select operation target: quit