Once the payment is made before the set date, the status of your invoice will change to Partially Paid. You can go ahead and add an Adjustment to the invoice manually for the remainder and save it. To add an adjustment:
Go to the Invoices module under Sales on the left sidebar
Open the specific invoice.
Click the Edit icon.
Scroll down and add the remaining amount as an Adjustment.
The status of the invoice will change to Paid.
Books
Simplify accounting
and GST filing.