I am just sitting the CIAO workshop and Alan Bundy and Michael Chan are talking about a very nice topic: the evolution of ontologies in Physics. They are applying this to historical examples like the latent heat problem and the MOND theory that is hot in Physics at the moment. The idea is that when experiments contradict theory, there is a clash between the theory ontology Ot and the sensory Ontology Os, which they solve by renaming apart selected concepts between the ontologies to resolve the contradiction. So they change the ontologies by renaming. The nice thing is that they can interpret the operation of renaming as a conservative theory extension which gives a nice interpretation of minimal theory change/repair.
You can find the details here.
Even though I totally buy into their observations, I think that it would be better to keep the theories as they are and interpret the repair operations as theory morphims. That would be a non-desctructive operation, and the operations would become very natural theory morphisms.