I am having the same problem and the question isn't answered yet. In the example, you showed three items with different prices on the estimate. On the invoice, you showed where one of them was 100% paid and didn't reflect on the invoice. However, could you show an example where a partial payment shows a percentage of the balance on an item that is reflected on the invoice?  For example, if one line item is paid in full, it doesn't show up on the following invoice, however, if it is a percentage of the total of that item, will the invoice reflect the unpaid balance?  It's not working for me and it is very confusing to my customers.