Argument from authority may be a logical fallacy, but science isn't primarily deductive in nature. Science is inductive, empirical and cumulative. You don't successfully attack science with logic. You add to the accumulation by discovering new stuff. You overturn paradigms by incorporating existing knowledge in more comprehensive paradigms.
Overturning a paradigm is one thing. An 'a priori' assumption, however is not a paradigm and is not reached inductively. It is assumed 'a priori' and overturning an 'a priori' assumption is impossible. That is the problem. Any 'new stuff' is still interpreted in the context of the 'a priori' assumtion, which never changes.
Therefore, while the paradigm may change, the 'a priori' assumption of naturalism does not. Ultimately, a naturalistic model (any model as long as it remains naturalistic) is assured.
Understand?