An option in addition to Richard's excellent suggestion is to create a debit memo in AR, apply the extra payment to it, then cut a check to the customer in Miscellaneous checks in the Banking module and document both transactions very well.
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An option in addition to Richard's excellent suggestion is to create a debit memo in AR, apply the extra payment to it, then cut a check to the customer in Miscellaneous checks in the Banking module and document both transactions very well.