Symptoms

The following error was caught when deploying a package

C:WindowsMicrosoft.NETFramework64v4.0.30319Microsoft.Common.targets(983,5): warning MSB3644: The reference assemblies for framework ".NETFramework,Version=v4.0" were not found. To resolve this, install the SDK or Targeting Pack for this framework version or retarget your application to a version of the framework for which you have the SDK or Targeting Pack installed. Note that assemblies will be resolved from the Global Assembly Cache (GAC) and will be used in place of reference assemblies. Therefore your assembly may not be correctly targeted for the framework you intend.
 

Diagnoses

The issue was with the referenced DLL within the BP process that was not using the proper .Net Target 4.0.

 

Resolution

Properly GAC'ed the assembly in the Prod environment, then the PandD tool deployed the complete .kspx file correctly without issues.