Your procedures are driven in large part by state law and your bank's capabilities for fixing account balances during the business day. There will be no generic procedures that would serve as evidence that your bank attempted good faith compliance; you need to write your own. This procedure will constitute a simple side track from your regular processes; it will be used a relatively small percentage of the time.
The best "policy" approach is to have a policy on the handling of third party claims against customer funds and to address this issue in a single paragraph.
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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.