how did you solve this?

Enter the AP credit invoice to the same job because that was over charged.  When they pay you back, enter a positive invoice in AP, not against the subcontract, but code it to the bank account you deposited the check.  This will act as the deposit.  Then apply the credit against the invoice with a manual check in AP that nets to zero.

I found the instructions in Help.  It's a 2-part entry 4-2 / Credit invoices and applying them to invoices

& Applying a vendor check to an outstanding accounts payable credit invoice.