Perhaps you could get the invoice from the sub, record it and apply the credit!

Since it looks like you are using Sage 300 CRE, I am going to move this post to the Sage Construction and Real Estate Support Group as this was posted in the incorrect forum.

Thanks,
Derek

You can enter a negative invoice for the credit they issued. You should request the invoice that you haven't received and enter that invoice as well. When you pay the open invoices for other jobs, also pay the negative invoice. The check amount will be reduced by the credit, the open invoices will be marked paid, and the negative invoice (credit) will show as paid, too.