my handwritten notes are not working as a method of documentation
They should. I think you have an examiner who's just looking for something to give you advice on. This pseudo requirement comes from a single sentence in the examination manual, not an actual regulatory requirement:
Banks should document SAR decisions, including the specific reason for filing or not filing a SAR.There is no length or weight requirement and the "reason" should be pretty simple; e.g. no SAR will be filed because although:
* we have a suspect, the amount involved is less than $5,000;
* the amount involved is $18,000, we have no suspect; or
* the amount of the transaction was unusually large, upon investigation we determined that it represented the ordinary course of the customer's business and, therefore, it was not suspicious.
You have to deal with whatever they put in the written report. If it's a sidebar conversation, you don't need to take advice unless you agree with it.