Amount showing on Adv Billing Report but not on Sales Order

We have an instance where two advanced billing invoices have been raised against one Sales Order.
The order has been shipped as per the two invoices so each invoice raised should have balanced to $0 with the adv bill balance applied.
When the second shipment invoice was raised, there was one line without the balance applied so to make it a $0 invoice I applied a 100% discount.
I now have the amount that should have come off the second invoice sitting on the advanced billing report however it is not showing on the SO as an advanced bill balance for me to be able to credit it off the SO?
When I try an Advanced Billing Credit Memo I get the message Amount entered cannot exceed Advance Deposit Billing Balance.

Has anyone else come across this or aware of any other way to clear an amount off the Adv Bill Report without doing a credit memo?

Were you able to get this figured out at some point? We’re running into the same issue.