Hi XX,
You need to execute the steps stated in the following document for your current NB5 backup domain:
http://seer.entsupport.symantec.com/docs/230047.htm
How to correctly decommission a NetBackup Media Server and remove it from the NetBackup environment
If the steps are not done, there'll be problem when executing bpmedialist, etc after the media server is removed from the domain and the problemn could be sticky to resolve.