I haven't been responsible for the NACHA-mandated annual self-audit, but I've done bank-mandated quarterly departmental audits, and on that level, one of the things that I really key in on is the documentation pertaining to changes to the ACH database (we're using a PEP+ system) and to any reversals or item/batch deletions or the resets of batch suspensions (due to risk limits or other factors). In my experience, it's critical that the ACH staff NEVER do anything to an item unless they have a piece of paper in their hands that gives them specific authorization to undertake the action. (I basically take the Teamster approach of "Hey, I don't even scratch my butt without a work order.") Phoned requests or other verbal requests shouldn't cut it. I don't even like using email requests--I prefer that dedicated forms be submitted and that the approvals come from known and authorized personnel.
I can't harp on this issue too much. I've been burned too often by customers trying to claim weeks later that they never told us to reverse an item or kill a batch or whatever. Always document your actions, and in your audit, pull some examples of reversals and deletions and resets and such and make certain that all the paperwork can be located.