over the past few years my backup servers have under gone numerous re-installs and re-names, just as they move from one site to the other or they are just too low spec server.
one of the things that started to bug be was that when you went to the drop down list to select a backup server it listed every server that you had had installed on your network.
I was recently on a backup course for Backup Exec 11d in reading and the course instructor mentioned to me how to do it, so I thought its about high time I posted it up here.
So first things first make sure all your backup jobs have finished running 
.
Then stop all services on all your backup servers. (Start you Backup Exec Console, Slick on the services and then enter in the name of the server of which you want to stop the services).
do that for all the servers that you have running.
Once you have stopped all Backup Services on all servers open up Active Directory Users and Computers, if you have not done so already enable the advance features from the View menu.
Then browse through the tree to Domain Name\Builtin\computers\ In there you should see an Object called BEserver and perhaps some other BEServer Objects with strange characters after them. if you delete those objects and then re-start all the services on all Backup Servers that should then recreate the BEServer object in AD and your List of server should only be what ever Backup Servers you have running live at that point in time.