Case Summary:

The old SCCM/SMS site has already been uninstalled in the server, but it still appear in ConfigMgr console

According to Microsoft Technet, if you need to start secondary site wizard, you may need to:

1- Navigate to System CenterConfiguration Manager / Site Database / Site Management / <site code> – <site name> / <secondary site code> – <secondary site name>

2- Right-click <secondary site code> and click delete.

But sometimes delete option is not available and reference to the old site still exist in Site Database.

Solution:

You need to open SQL Enterprise Manager console on server that host SMS/SCCM Database, and select correct database and run the following queries to delete any reference to the old site

DELETE FROM SysResList WHERE SiteCode = ‘XXX’

DELETE FROM SiteBoundaryADSite WHERE SiteCode = ‘XXX’

DELETE FROM SiteBoundaryIPSubnet WHERE SiteCode = ‘XXX’

DELETE FROM SiteControl WHERE SiteCode = ‘XXX’

DELETE FROM SiteControlNotification WHERE SiteCode = ‘XXX’

DELETE FROM Sites WHERE SiteCode = ‘XXX’

DELETE FROM Sites_DATA WHERE SiteCode = ‘XXX’

DELETE FROM SiteWork WHERE SiteCode = ‘XXX’

DELETE FROM PkgServers WHERE sitecode = ‘XXX’

DELETE FROM PkgStatus WHERE sitecode = ‘XXX’

Note: Change XXX to secondary site code

Best Regards