Issue
When deploying a package to its target environment over a previously deployed application, there may be a reference error thrown on one or more SmartObjects.
After right-clicking the SmartOjects with the error and selecting "Configure", there will be a "System Name" conflict and the GUIDs of the source and target SmartObject will be different. Typically these GUIDs should match for objects that have previously been deployed to the target environment.
The change in object GUIDs during deployment is currently as designed. When deploying non-SharePoint artifacts contained in a package where a SharePoint-integrated solution is also used, it will run a refactor on all objects in the package, giving them a new GUID on the target. This is to align with the "Deploy As New" functionality of P&D, where users may deploy a copy of a SharePoint integrated solution to the same source environment but with different target SharePoint site. When deploying non-SharePoint artifacts on their own as a package, the "Deploy As New" functionality won't kick in and in this scenario, the package will end up with a GUID mismatch and be blocked from deployment.
Resolution
To keep the GUIDs the same, create a new package containing any associated SharePoint artifacts along with the original objects you were attempting to deploy. You can then deselect any of these SharePoint components at deployment if you do not wish to make any changes to these. This will allow the "Deploy As New" functionality to kick in and avoid the GUID mismatch issue.
