Why did the status of a prepayment invoice be displayed as unpaid?

Though prepayment is paid partially the status is shown as unpaid on the invoice workbench. This is intended behavior. A prepayment invoice can be paid partially but it can't be applied to standard invoice or expense report.

In order for you to apply a prepayment to a standard invoice or expense report it must be fully paid. Until it's fully paid, the status of the prepayment remains as unpaid.