I would ask your auditor. Reg D gives you the option of rejecting items that exceed transaction limitations or adopting a process to honor transactions and notify customers that exceed limits, as well as either close or reclassify accounts that exceed limits more than 3 times in a rolling 12 month period.
Your auditors may be more familiar with the second option since it is the one that most banks use.
Are these internal auditors, outsourced third party? If the latter, maybe you need to vet them at a little more...
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