Problem:
I am trying to delete a Secondary Site from my hierarchy. However, when I right-click on the Site in the Admin Console on my Central Site why don’t I see the “Delete” option?
Resolution:
This is because you can only Delete a Secondary Site from an Administrator Console that is connected directly to the Secondary Site’s Parent Primary Site. It is not supported to delete a Secondary Site from any other Administrator Console/ Site.
To prove the point load the SMS Administrator Console and connect to your Central Site. Navigate to:
Systems Management Server
|- Site Database (<site_code> – <site_description>)
|-Site Hierarchy
|-Central Site
|-Primary Site
|- Secondary
Right-click the Secondary Site and you’ll see the following items on the context menu:

Now within the same Admin Console add a new connection (if one doesn’t exist already), to the Parent Primary Site of the Secondary you are trying to delete. Again navigate to:
Systems Management Server
|- Site Database (<site_code> – <site_description>)
|-Site Hierarchy
|-Primary Site
|- Secondary
Right-click the same Secondary Site but this time you’ll see the “Delete” item on the context menu:

If you choose the “Delete” option it will start the “Delete Secondary Site Wizard” which gives you the option of either Deleting the Site or Deinstalling it (deleting simply deletes it from the Administrator Console but leaves SMS installed on the Secondary, whereas Deinstall will remove SMS from the Secondary and delete it from the Admin Console).
