Currently the cloning is based on setting OldPrimaryKey to each newly cloned mode node item. It’s a bit hidden there, and it’s not persisted. The mapping is used in updateReferences(). If someone or something invalidates model cache in between calling Clone() and UpdateReferences(), it breaks the functionality, because model is loaded from the disk without OldPrimaryKey set. Moreover, the complexity of UpdateReferences() operation is n^2.
refactoring:
Clone() would return Dictionary<Guid,Guid> primaryKeyMapping having oldPrimaryKey as a key and newPrimaryKey as a value. PrimaryKeyMapping would be passed into UpdateReferences(). Complexity should drop to nlog(n).