I also have this issue. Have a lot of SuperAgent repositories, some for machines that no longer exist. Have removed functionality for all machines, but they still exist. Have tried cleaning out the xml files, but it keeps recreating them.
the SA repo will automatically delete when the machine checks back in to ePO with the property of bEnableSuprtAgentRepository returns 0. If the machine never reports back in, then this property won't be set. You can try deleting the machine from the system tree (dont' check remove agent) and then cycle the ePO services. If that still doesn't work, You will have to manually edit the SiteMgr.xml to remove the element for that repo.
I would be EXTREMELY careful in editing the SiteMgr.xml. You can cause serious issues if you don't do it properly. Make sure you stop the ePO services while editing it and backup a copy of the file before editing it.
If the machine(s) which are configured by Agent Policy are no longer reporting back to ePO, then changing the policy will have no affect (the SA repository entry would remain). Refer to KB60470 for removing the defunct Super Agent repositories.
The computer hosting the SuperAgent repository was removed from the network without first uninstalling the agent. Because the agent was never successfully removed first from the computer, the SiteList.xml file still lists this non-active SuperAgent repository entry.
The computer was deleted from the ePO system tree, with the option to Uninstall the agent selected. This marks the computer as Type 24 in the ePO database, forcing the agent has to call back to the ePO server for the entry to be removed from the database. This will not happen since the computer is no longer available in the network
This works for me, thanks. I looked at that before, but it didn't click that I needed to remove the clients with the uninstall option checked. Removed the 5 I tested it with.