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.
Though prepayment is paid partially the status is shown as unpaid on the invoice workbench. This is intended behavior.
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Why never which recognized which another drop-out 25-cent not displaying also unpaid?