From the guidance you cite:
The Agencies expect financial institutions to adopt deposit reconciliation policies and practices that are designed to avoid or reconcile discrepancies, or designed to resolve discrepancies such that customers are not disadvantaged.
They are not suggesting that your "policies" and "practices" need to be in writing. If you correct an errant deposit and give customer credit for the actual amount of items deposited in a time frame consistent with Regulation CC that's both your policy and your practice.
This particular fad came from a single instance where a bank promised one thing in its contract, but did something else in practice. The Interagency "guidance" is overblown.
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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.