Also, unless these loans are fully documented with notes, loan agreements, etc., this probably amounts to a significant enough co-mingling of funds that each business is no longer considered independent and a combined CTR filing should be considered.
While the regulators are encouraging banks to bank MSB, with about a 100, you are more than doing your part. If they cannot fully explain these transactions and you don't fully understand them from a logical perspective, I would be looking at getting rid of my problem children.
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