When you install patches on an instance of Microsoft SQL Server 2014 or 2016 that contains lots of databases, the setup may fail. And you may receive the following error message:
Microsoft.SqlServer.Configuration.SqlEngine.SqlEngineConfigException: Failed to shutdown the instance with process ID xxxx. Error encountered: Microsoft.SqlServer.Configuration.Sco.ScoException: The service cannot accept control messages at this time.
Note After you apply this fix, the patch setup program will wait for SQL Server to stop up to 30 minutes. If more than 30 minutes SQL Server is still stopping, patch setup may still fail.
Microsoft has confirmed that this is a problem in the Microsoft products that are listed in the "Applies to" section.