very interesting subject, and many factors to consider. What are the insurance co requirements ? they certainly don't want another fire after the rebuild process.
What has always bugged me is a meg of wires after lightning but what else do you do other than open the walls? In truth, the cable could be busted wide open and insulation missing but the air gap (or remaining insulation) might give an acceptable insulation reading. Might a TDR show anything valuable in that case (maybe you would have to have some violent physical results present from the lightning)? How do you test for possible lightning damage other than a meg test?
Why argue with the architect?
If you are going to be paid to replace the cables, take the money and be happy.
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Answers based on 2011 NEC
We have had customers say replace after we complete testing and everything is 100% acceptable. They have the cash and want to part with it. by all means go with it.
We had a job where the customer had us do just that, when the insurance company saw our test reports they refused to pay the customer. What finally happened I have no idea as we explained to the customer, he told us to replace based on our data, he was liable for paying, case closed as far as I am concerned.