Sometimes, if you have a site system crash and it’s unrecoverable, it can be a challenge to remove the site system from ConfigMgr. After 24 hours, the system should remove the last role (Component Server) and allow you to remove the system from the ConfigMgr console. If you don’t have 24 hours to wait, there’s a shortcut you can use. Be advised, this is not Microsoft supported, but it seems to work well.
First, remove all roles from the site system. You should be left with nothing but the Component Server and Site System roles. The system does not allow you to delete the system until the Component Server role is gone. You can normally restart the SMS_SITE_COMPONENT_MANAGER, but if the site system is no longer online, this will not clear the old entry.
After you have removed all of the roles, login to your primary site server. Open Registry Editor and navigate to HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\SMS\SMS_SITE_COMPONENT_MANAGER\Component Servers. Under this key, locate the orphaned site system. Expand it’s key, then the Components key. For each listed component, set the “Deinstallation Start Time” REG_DWORD value to 1.
Now, at the very least, restart SMS_SITE_COMPONENT_MANAGER. I recommend restarting the server, but you at least need to restart the component manager. After a few minutes, the Component Server role should clear out and you can delete the site system. If you look in the sitecomp.log, you should see these entries:
That tells you that the system considers the components uninstalled. Setting the deinstallation start time to 1 makes it exceed the retry interval.
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