This will for sure add back end complexity. I really think the best solution for now if a down payment is required is to use separate invoices for example you have the original invoice then the down payment invoice and in the Description you can say Down payment for Invoice #XXX.
At some point this would be nice, but at the same time we also don't want to over complicate the back end code.
If anyone is willing to take a stab at this and issue a pull Request: see here for Contributing to ITFlow:
https://docs.itflow.org/contribute