Emily,
In your abstract, you state that:
"scientific enquiry has presupposed a relatively simple relationship between our empirical evidence and the facts of reality... Such assumptions seem to be necessary... But developments ... give us specific reasons to question these assumptions."
The simple relationship between evidence and reality, need not be questioned. Physical theories merely produce numerical predictions, that either agree or disagree with observations. They do nothing else. In particular, they provide no evidence, either for or against, all the metaphysical "interpretations" that have the attached to the theories. The theories can do little more than "fit curves to data", and they can only even do that, in cases where the data has an extremely low information content - that is what makes the data "predictable", by the theory, in the first place.
Since the "interpretations of the theory" invariably have a higher information content than the theories themselves, the "interpretations" cannot possibly be contained within the theories themselves; they have simply been made-up and slapped-on. Hence, while experiments may confirm that the theory "fits" the data, they cannot provide any evidence that the "interpretation" fits the theory.
Rather than questioning the "reliability of memories", physicists need to question the "meaning" and "significance" that they have attached to them.