On a commercial loan I would make sure I looked at the Note and/or security agreement before doing anything. On some commercial deals, the borrower either can't prepay principal at all or it has to be paid in a certain amount (eg. you may prepay principal at any time, however, any such prepayment must be in an amount at least equal to X").
I would also check and make sure allowing this wouldn't mess up the amortization schedule for the loan. A long shot, I admit.