Specifically, did you see any errors when this was upgrading the database?
The scenario you have decribed is what you would see if the clients were attempting to connect to a SEE Management Server whose keys (stored within the database) have changed.
To resolve this (if this is indeed the issue) you will need to install and run the OTP key changer on the server, adn run the resultant msi on your clients.
Do you have a backup copy of your SEEMSDb? The important bit is the DeploymentKeys table...