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How to apply Prepayment on an Invoice with Discount

Prepayment question:

Original Invoice: INV1: $1000 payment term: 2/10 Net 30. Inv date: Jun 1.
Today is Jun 4
User makes a prepayment for $980 ($1000-2% of 1000).

When the real Invoice INV1 is ready to be applied, would the prepayment be applied as $980 or $1000? If $980, then, will the PO remain open?

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