Why is my advance payment not deducted in the final invoice?

Has the advance invoice been assigned to a final invoise?
The amount can only be deducted if the advance invoice is assigned to a final invoice.

Right-click on the final invoice in the side navigation of the event (context menu) and select Assign open advance invoice.

Is the advance invoice marked as "paid"?
The amount can only be deducted if a payment has been entered for the advance invoice.

Go to the advance invoice in the side navigation and select  Payments. Enter any payments you have received. The invoice status will change to “Paid" automatically, once the full sum has been entered as payment received. Alternatively, change the status of the advance invoice to "Paid" manually in the top part of the invoice input window.