You can use the Remote Agent Utility to remove a media server so that the Remote Agent no longer publishes information to it.
See About publishing the Remote Agent for Windows Systems to media servers.
To remove media servers that the Remote Agent can publish to
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On the computer on which the Remote Agent is installed, on the taskbar, click Start > All Programs > Symantec Backup Exec > Backup Exec 2010 Remote Agent Utility.
When the Remote Agent Utility is running, an icon appears in the system tray. You can double-click this icon to view the utility.
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Select the media server that you want to remove from the list.