Symptoms
The SmartObjects which are said to be missing have already been mapped to existing artifacts on the target server but it still ends up with an error.
Once mapped, it will show this under Missing References:
this_source_smartobject (this_target_smartobject)
Diagnoses
The SmartObjects were repackaged on the source environment and redeployed to the target environment. After re-mapping the new versions of the SmartObjects, the missing references were resolved.
Resolution
The dev smartobjects were repackaged and redeployed to QA. After re-mapping the new versions of the smartobjects, the missing references were resolved.