To clean up metadata

1. At the command line, type Ntdsutil and press ENTER.

C:\WINDOWS>ntdsutil
ntdsutil:

1. At the Ntdsutil: prompt, type metadata cleanup and press Enter.

ntdsutil: metadata cleanup
metadata cleanup:

1. At the metadata cleanup: prompt, type connections and press Enter.

metadata cleanup: connections
server connections:

1. At the server connections: prompt, type connect to server <servername>, where <servername> is the domain controller (any functional domain controller in the same domain) from which you plan to clean up the metadata of the failed domain controller. Press Enter.

server connections: connect to server server100
Binding to server100 ...
Connected to server100 using credentials of locally logged on user.
server connections:

Note: Windows Server 2003 Service Pack 1 eliminates the need for the above step.

1. Type quit and press Enter to return you to the metadata cleanup: prompt.

server connections: q
metadata cleanup:

1. Type select operation target and press Enter.

metadata cleanup: Select operation target
select operation target:

1. Type list domains and press Enter. This lists all domains in the forest with a number associated with each.

select operation target: list domains
Found 1 domain(s)
0 - DC=dpetri,DC=net
select operation target:

1. Type select domain <number>, where <number> is the number corresponding to the domain in which the failed server was located. Press Enter.

select operation target: Select domain 0
No current site
Domain - DC=dpetri,DC=net
No current server
No current Naming Context
select operation target:

1. Type list sites and press Enter.

select operation target: List sites
Found 1 site(s)
0 - CN=Default-First-Site-Name,CN=Sites,CN=Configuration,DC=dpetri,DC=net
select operation target:

1. Type select site <number>, where <number> refers to the number of the site in which the domain controller was a member. Press Enter.

select operation target: Select site 0
Site - CN=Default-First-Site-Name,CN=Sites,CN=Configuration,DC=dpetri,DC=net
Domain - DC=dpetri,DC=net
No current server
No current Naming Context
select operation target:

1. Type list servers in site and press Enter. This will list all servers in that site with a corresponding number.

select operation target: List servers in site
Found 2 server(s)
0 - CN=SERVER200,CN=Servers,CN=Default-First-Site-Name,CN=Sites,CN=Configuration,DC=dpetri,DC=net
1 - CN=SERVER100,CN=Servers,CN=Default-First-Site-Name,CN=Sites,CN=Configuration,DC=dpetri,DC=net
select operation target:

1. Type select server <number> and press Enter, where <number> refers to the domain controller to be removed.

select operation target: Select server 0
Site - CN=Default-First-Site-Name,CN=Sites,CN=Configuration,DC=dpetri,DC=net
Domain - DC=dpetri,DC=net
Server - CN=SERVER200,CN=Servers,CN=Default-First-Site-Name,CN=Sites,CN=Configuration,DC=dpetri,DC=net
 DSA object - CN=NTDS Settings,CN=SERVER200,CN=Servers,CN=Default-First-Site-Name,CN=Sites,CN=Configuration,DC=dpetri,DC=net
 DNS host name - server200.dpetri.net
 Computer object - CN=SERVER200,OU=Domain Controllers,DC=dpetri,DC=net
No current Naming Context
select operation target:

1. Type quit and press Enter. The Metadata cleanup menu is displayed.

select operation target: q
metadata cleanup:

1. Type remove selected server and press Enter.

You will receive a warning message. Read it, and if you agree, press Yes.

metadata cleanup: Remove selected server

"CN=SERVER200,CN=Servers,CN=Default-First-Site-Name,CN=Sites,CN=Configuration,DC=dpetri,DC=net" removed from server "server100"
metadata cleanup:

At this point, Active Directory confirms that the domain controller was removed successfully. If you receive an error that the object could not be found, Active Directory might have already removed from the domain controller.

Crédito : http://www.petri.co.il/delete_failed_dcs_from_ad.htm