Working at a customer, doing an in place upgrade from Windows Server 2008 R2 server with ConfigMgr 1606 to Windows Server 2016.

After the upgrade a connection to the ConfigMgr cannot be made using the console, investigating it and we found out that the Root\SMS namespace has gone, (even running as system it was not to find)

Asking around, no one have seen this, but my friend Johan Arwidmark sent an email to the product team, and the reply was easy to understand (yet, undocumented)

You do need to do a site reset after an OS upgrade, and after that, it all works like a charm

Here is some guidance to doing such upgrade, just don’t forget to run a site reset.

http://ccmexec.com/2016/03/configmgr-cb-1602-server-2008-r2-in-place-upgrade-to-2012-r2/

https://technet.microsoft.com/library/hh852345.aspx

/mike