Papers on Prolog-like languages without closed world assumption (CWA)
Thank you for a great question! I am looking into papers on related subjects myself--I'll post anything worthwhile that I come across, and would appreciate if you would do the same. = ) Off the top of my head, you might be interested in ileanTAP, a Prolog theorem prover for intuitionistic logic (includes a short paper). Just so the term is not left undefined:


  Intuitionistic logic, or constructive logic, is a symbolic logic system
  differing from classical logic in its definition of the meaning of a statement 
  being true. In classical logic, all well-formed statements are assumed to be 
  either true or false, even if we do not have a proof of either. In constructive
  logic, a statement is 'only true' if there is a constructive proof that it is
  true, and 'only false' if there is a constructive proof that it is false.
  Operations in constructive logic preserve justification, rather than truth. (Wikipedia)


Have you read Kuhn on scientific paradigm shifts? The problem you have described is generally applicable to all of science: theories (and coherent theoretical domains) are abstracted axiomatic systems, and updating a scientific domain (as opposed to "filling out the missing bits" by using what's already established as "axioms") requires switching from one isomorphic system to another (two systems are isomorphic if they have identical or similar outputs for some narrow set of parameters, e.g. Newtonian physics and GR).