Hi Kedalene,
1. When you create AR invoice, system automatically links fully paid down payment amount. Not sure, how did you miss or forgotten?
2. a) Create AR credit memo for AR invoice. so that SO will open
b) Cancel incoming payment will open AR down payment request document
c) Create again incoming payment for re-opened AR down payment
d) From re-opened sales order, create AR invoice and then add down payment amount.
Better check it test DB.
Thanks & Regards,
Nagarajan