I have a prepayment that was applied to a SO. For some reason the correct amount of money was not transferred to an invoice, and I had to manually apply part of the prepayment to the invoice document. But now the “transferred to invoice” total does not equal the same amounts of all invoices (that are paid via that prepayment) Below are some screenshots
Prepayment:

Application History:

As you can tell there is a remaining balance and applied to order but the sales order still has an awaiting payment status.