You say that your son set up the minimum payment arrangement "many years ago", but that "over the years he had cleared payments before interest could be charged to his cards."
So in effect, the minimum payment has never operated. The bank discarded the mandate because it hadn't been used. It sounds odd to me, I haven't encountered this situation before. If the bank says it sent a letter on a specific date the chances are very high that it did, and seeing a copy of it isn't really going to alter the situation.
Your son needs to talk to the bank to resolve this - the bank can remove the late-payment strike from his credit record, if they agree that there are grounds for doing so.
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