This paper presents a rule based approach to ontology refactoring. Our method supports large scale instance relationships for support of translation to an improved, functionally equivalent design. By generating new ontology versions on-the-fly we can verify potential updates to our requirements. An example of this technique is presented utilizing a subset of the OWL-DL specification through the implementation of the Jena API. Advantages of this approach include rapid prototyping, versioning support, querying and tool development to support the automated engineering of instance data.