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Why is the destination feature class being unregistered as versioned when the origin feature class is being unregistered as versioned?
If the Unregister As Versioned command is executed on a non-attributed relationship class object, the origin and destination classes in that relationship are also unregistered as versioned.
When executing the Unregister As Versioned command against a feature dataset, the command is called on all classes within the feature dataset. When Unregister as Versioned is called on a relationship class, it propagates that call to both the origin and destination objects within the relationship. The end result in all cases, when unregistering a relationship class as versioned, is that both the origin and destination objects in the relationship are unregistered as versioned, even if the objects are located in different feature datasets.
It is the data owner’s responsibility to understand how the Unregister As Versioned command behaves, because once a class has been unregistered as versioned it cannot be undone unless the database is restored from backup.