It sounds like the correct quantity has been invoice but not the right Amount for payment? If so, I would suggest looking at treating as an incorrect invoice, crediting it off and re-issuing the invoice. I believe NS generally clocks that the quantity has been billed in full but doesn't recognize that you didn't bill it for the same amount, so treats it as fully billed.
If it was s'posed to be a partial bill, the quantity should be reduced so that the amount reduces with it, not overwriting the amount. But depends how you bill items - I don't know if the below helps?
https://suiteanswers.custhelp.com/app/answers/detail/a_id/33409/loc/en_US