OK..
I am confused.. you are saying that you had a working environment when on Version 11.6?
Though when you upgraded the agents AND the server to 12.0, that it broke the Console, but the agents are still blocking?
If this is the case I would open a support ticket.. there is a lot more things happening on the back end of the server then.
Sounds like the upgrade went bad.
I do know that there is a wierd known issue where the UI has broke before after an upgrade. The resolution it to uninstall the Enforce Console and reinstall the 12.0 Version of the platform. Make sure to back up the crypto master key file before uninstalling (backup the config drive) and DO NOT reinitialize the DB when installing the Version 12 platform.
Overall I would open a support case and see what they say.
Hope this makes sense.
If this solves your questions please marked as solved.
Ronak