I assume you mean that you have one job which backs up multiple servers, rather than just one job which backs up that one server which is no longer there?
If so then what you need to do is go into the backup selections section of the backup job, and then switch from graphical display to text display. This will show you the actual list of backup selections used by Backup Exec, unlike the graphical version which will show you the information only as long as the relevant server or folder is still there. You can then delete all the relevant lines from the text display which relate to the server you want to remove.
