You can delete the payment associated with the invoice by getting into the "Payments Received" sub-tab under the "Invoices" tab. Refer the following image:
Zoho Invoice FAQ
© 2013, ZOHO Corp. Invoice Software 4900 Hopyard Rd, Suite 310, Pleasanton, CA 94588, USA Support: +1 888-900-9646 | Sales: +1 888-204-3539,