Main evidence is that near and far UV CD and trap fluorescence is unchanged.
This is useful and consistent with no major unfolding, but is not high resolution. More definitive would be X-ray crystallography, but much more work and has some limitations of its own. Note that the correctness of the DNA sequence and the mass as determined by mass spectrometry addresses whether or not they had the correct polypeptide, not whether it was folded properly - although on relooking at the wording of the question, it could also be read to include this. Limitation is that changing amino acids often effects other aspects of catalysis as well. Can see this as non-additivity of the two Arg substitutions.