As suggested, your customer told you a story. That does not affect how you complete the CTR.
Nor will it affect the way a third party, regulator or auditor, evaluates whether or not your bank should have filed a SAR based on the fact that the activity is apparently inconsistent with your customer's business, particularly if the "specific denomination" is $100 bills.
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In this world you must be oh so smart or oh so pleasant. Well, for years I was smart. I recommend pleasant.