I thought that this might be what you want: https://quickbooks.intuit.com/learn-support/en-us/help-article/invoicing/set-send-progress-invoices-... 

I was trying to figure out a graceful way to send partial shipments while keeping the invoice and packing list tightly coupled.

EDIT: After trying this feature out, it looks like this only allows % or the $ amount to ship, and oddly doesn't have a way to edit the qty shipped.

I ended up having to copy the estimate my customer accepted, edit the qty to match what was being shipped, and then create the invoice.  Not what I was hoping for, and it likely won't work for you either..