If the loan agreement contains language about right of setoff, you may be able to debit his checking account. However, if you do, I would still reverse the loan payment however you would normally do so, and then do an advice of charge against the checking account with the loan payment transaction, with notations as to the situation. This way you have an audit trail of what actually occured.
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I hear and I forget. I see and I remember. I do and I understand.--Confucius