I have many clients who still have a significant amount of money left in their deposit accounts for payments that piled up over a time long past. How do I manually clear this amount down to $0.00 so that it doesn't look on their invoices like I still owe them money?
You can use the Refund Deposit Amount option in the payment mode dropdown box. Then check the Pre Payment Deposit option and enter the amount. The Remarks section can be used to record internal notes (not seen by the client) for tracking purposes. See example in screenshot below.