How partial payment of Invoices works
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When an invoice is paid in part. The original invoice is split into 2 invoices. One of which is fully paid and the other is completely unpaid.
This article demonstrates what occurs when an invoice with three items is partially paid
The following invoice has three items

The invoice has been assigned an invoice Ref of 33

Click on the Payment button

By default ALL three items are selected with the full outstanding amounts entered in the payment details

Here we have not paid all items in full

1) The first entry has been paid in full
2) The second entry has been partially paid
3) The third entry has not been paid at all
The result is Two Invoices – One fully paid and the other completely unpaid

1) The new paid invoice is give a new reference “33/Part Paid”
2) The unpaid section of the invoice retains the original reference