Symptoms

After upgrading to 4.6.9 from 4.6.6 or later, Package and Deploy packages that used to be able to be packaged before upgrade no longer can be packaged. Errors regarding missing references for smartobject properties are thrown, and the properties the errors are being thrown for have never existed for the smartobject.
 

Diagnoses

This was found to be a problem with smartobjects that had associations with other smartobjects and Package and Deploy. PandD would look at the associated smartobject properties instead of the smartobjects needed for the project and throw missing references for the associated properties when they were never meant to be a part of the package.
 

Resolution

This is a known issue, and the following workaround has worked:

If you edit the view, and subsequently the “When the view executed initialized” rule, and just click on "OK" and then "Finish", everything seems to work when you attempt to repackage the form. If the smartobject is called somewhere else in the rules, you will need to do the same thing for the rule that contains the smartobject call for one of the smartobjects throwing the error in Package and Deploy.

The following bug has also been logged for this behavior:

Bug 466163 - SF - SmartObject Associations which was removed still present in View/Form XML. PandD then wants to package the unused SMO as a dependency. (SmartObject)