Category: Secondary Sites

How to Uninstall SCCM2012 Secondary Site Manually

Today I was working with a customer upgrading their System Center suite from 2012 SP1 to R2 when we got totally thrown off track by being unable to install the Secondary site back to the server we deleted it from earlier.

Earlier in the upgrade process we decided it was best to remove the secondary site and re-deploy it after the upgrade and it would be the cleanest way of doing it.


When you remove a secondary site the SCCM Console gives you two options:

  • Uninstall the Secondary site


  • Delete the Secondary site


We selected to use Delete. This is where we went wrong.

Deleting a secondary site removes the secondary site from the primary but it does NOT uninstall the secondary site installation from the secondary server. The secondary server thinks it is still running fine but the primary has gone offline.

We then wanted to upgrade or re-install the secondary on the same server but the installer told us that the CONFIGMGRSEC database still existed and could not be used.

At this point there is no simple way to re-connect and upgrade the secondary site.

I then found this fantastic blog post that Phyllis in IT has written: How to uninstall SCCM2012 Secondary Site manually.

In short, from the Secondary server run C:\Program Files\Microsoft Configuration Manager\bin\X64\SETUP /DEINSTALL from an elevated command prompt.

To track it’s progress, watch the smstsvc and ConfigMgrSetup log files located on the C:\ of the Secondary server. SQL Server Express should be uninstalled as part of this process and the whole thing takes about 30 minutes.

Once the uninstall is complete, also uninstall the VC Redistributable because the installer will attempt to install the VC Redistributable and the installer will do a repair instead of an install and return an error code 3010 which is the installer error for “needs a reboot”.

Make sure you reboot the server before re-installing the secondary site.

So the lesson to learn is “Never select Delete the Secondary site from the console!” – Unless you no longer want your Secondary server and are going to decommission the whole server.

Thanks to Shayne for all his support and being the worlds best customer and a great friend.
And thanks to Phyllis in IT for the great blog post that got the final answer.