There is a primary checkbox on the core screen that impacts how an invoice shows the reman/core, and whether the core is automatically added to the invoice or whether it has to be keyed. Please refer to this document for examples:
Note: When you invoice a reman part the invoice that gets generated online versus the one that goes into history COULD be different if the core part is changed between the original print and the billing run.
There is also a setting in COTAB to 'SUBTRACT CORE AMOUNT FROM REMAN PRICE' but it only impacts the parts availability screens, not invoices. Consult the online help for the COTAB Configuration Table information.