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I opened a similar ideas. Please update us on this topic.
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Just when I thought I had thought of a solution, I find out that it is impossible. If we wait a little longer we will have been asking for this for ten years.
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I think the accounting could get messy. If people could unapply or change how much was applied, you could end up with wacky amounts staying in the Prepayment Account. Typically, when an Invoice is posted for a PO with a prepayment, the distributions would be: Debit: Accrued Purchase AccountCredit: PO Prepayment Account (if total is less than amount prepaid, the balance of the prepay would be available for the next invoice)Credit: AP Account (Only gets hit if the Invoice total is greater than the amount of the prepay).If you were able to unapply, you would need to have an apply window added during the Enter/Match window...and the Shipment/Invoice window. I could think of some "work arounds" but I think security and reconciliation would get really messy if this was changed.
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Setting under: Purchasing>Setup>Purchase Order Processing…scroll down checkbox Warn if PO Line is not fully invoiced. (I recommend people add a password if they want to prevent)