Hi,
Yes you can remove the Decommission DC from AD. First run the following command see is there any FSMO roles resides on that DC. If yes kindly Transfer or Seized the role.
Net dom Query Fsmo
Once you have done the above steps then download the script from below link for metadata clean-up.
https://gallery.technet.microsoft.com/scriptcenter/d31f091f-2642-4ede-9f97-0e1cc4d577f3
Copy the code in notepad and save as metadatacleanup.vbs and then open the command prompt run as administrator on one of DC and go to the path where you have copied the script and then run the command cscript
metadatacleanup.vbs
It will ask for Domain controller name which you want to remove just type Decommission DC name and then script will remove automatically. Once this is done you have to remove Decommission DC from DNS manually as given below.
Manual Steps
Dnsmgmt.msc [Dns Management]
A.Expand the forward lookup zones\_msdcs folder
i. Make sure only the actual domain controllers are listed, delete wrong Alias recordsremove wrong name server records
ii. Select the container [forward lookup zones\_msdcs.domain.com\dc\_sites_\sitename\_tcp] > delete incorrect _ldap and _kerberos records are listed.
iii. Select the container [forward lookup zones\_msdcs.domain.com\dc\_tcp] and delete incorrect _ldap and _kerberos records
iv. Expand the [forward lookup zones\_msdcs.domain.com\domains\guid\_tcp] and delete incorrect _ldap entries
v. Select [forward lookup zones\_msdcs.domain.com\gc] delete incorrect HostA records
vi. Expand the [forward lookup zones\_msdcs.domain.com\gc\_sites\sitename\_tcp] delete incorrect _ldap entries
vii.Select the [forward lookup zones\_msdcs.domain.com\gc\_tcp] delete incorrect _ldap entries
viii. Select the [forward lookup zones\_msdcs.domain.com\pdc\_tcp] delete incorrect _ldap entries
B.Expand the forward lookup zones\domain.com folder
i.Delete Host(A) records of dcs which are non-existant.
ii.Correct the NameServer (NS) records
iii. Follow steps similar to A ii >> A viii
Dssite.msc [Sites and Services]
A.Expand the [Sites\Sitename\Servers] delete incorrect servers
B.Delete incorrect subnet configurations [Sites\Subnets]
C.Delete incorrect site links [Sites\IP]
Make sure the domain controllers are pointing to the correct dns servers in tcp\ip settings.
Force replication repadmin /syncall