Symptoms
After deleting a service instance, editing a view containing references to SmartObjects that use the deleted service instance throws a "Root element is missing" error, and the view cannot be edited.
Diagnoses
A bug has been logged against this behavior.
Resolution
Locate the GUID for the deleted Service Instance and recreate it. This will allow you to edit the view and replace the erroring Smartobjects with the correct SmartObjects. After that, you can once again delete the service instance.