Symptoms

After upgrading from 4.6.9 to 4.6.11, there were some strange errors in the log file, like this:

10:4: PatchPanel.Patch: 10:48:41:andgtandgt Logged Error: SQL execution disabled, database was not previously upgraded to at least 4.6.9
10:5: PatchHelper.FlagSqlTargetsToNotInstall: 10:42:32:andgtandgt Logged Error: SQL execution disabled, database was not previously upgraded to at least 4.6.9

There is also one logged warning:

10:4: PatchPanel.Patch: 10:50:42:andgtandgt Logged Warning: DB versions not updated, sql scripts not set to execute.

However, after the upgrade everything seemed normal. After a while though when we tested Package and Deployment and tried to deploy a package, it came up with this error:

System.Exception: This package was created using a newer version of K2. Upgrade your K2 server before deploying this package.
at SourceCode.Management.Controls.DeploySelectPackage.ValidatePackageVersion(ClientSession clientSession)
at SourceCode.Management.Controls.DeploySelectPackage.Finish()
 

Diagnoses

We noticed that in Programs and Features there were two installations of "K2 Server for SharePoint 2013", "K2 SmartForms for SharePoint 2013" and "K2 Workspace for SharePoint 2013". So there were version discrepancies between those three items (two versions of each were installed).
 

Resolution

The solution to this was that we ran the K2 SmartForms Setup Manager and the K2 for SharePoint Setup Manager and did a reconfiguration on each. Finally Package and Deployment was working now.