I'd recommend being careful about using "uncooperative bank" as an exception reason. We use to have an exception reason of "could not verify check" and our OCC examiners said that was not a valid exception reason. They said that just because the bank would not verify the check did not mean there was a valid reason to believe that the check was uncollectible. My understanding of the regulation in relation to your original question is that an extended hold can be put on after the fact only if you become aware of additional facts that you were not aware of at the time of the deposit that makes you think the checks won't be paid. You didn't indicate that additional facts had been obtained, so I don't think applying an extended hold would be allowed.
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