I just updated my LAB Environment to System Center 2012 Configuration Manager R2, and after the Installation I wasn’t able to Connect with the Console. I got the error
Configuration Manager cannot connect to the site …
Configuration Manager Console cannot connect to the Configuration Manager Site Database. Verify the following:
I assumed, that the console wouldn’t be updated through the process. I then tried to start the Installation process through the Setup Routine with $SCCMInstallationFolder\Tools\ConsoleSetup\ConsoleSetup.exe, but I received an error. I then executed the MSI, $SCCMInstallationFolder\Tools\ConsoleSetup\AdminConsole.msi, directly, and it allowed me to repair the Installation. After the Repair, a connect to the site was successful, and I could manage the new Features.
Hope this helps, Martin.