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Delete of Creo objects (EPMDocument) should be possible even if there are creo internal relationships between different Creo objects. Otherwise it's not possible to cleanup the Creo database.
By today the user has to do following:
If dependencies exist between CAD Documents (internal or not), in order to preserve data consistency it is not possible to delete the parents in PDM system and the CAD application remains the master. So you will need to first remove the dependency within the CAD application, purge the old iterations before deleting the wanted references.
Idea created by Roland Kupferschmitt, ABB