Closing part-paid invoices/ dealing with intermediary commissions

Is there a way to close partly paid invoices?

I have an invoice open that I consider paid but I only received around 97% of the value and don't want to book the whole amount as received (=income).

This actually happens quite a lot- you invoice a client and they make a bank transfer but an intermediary bank takes a commission before it hits your bank and you receive less than the amount billed. It would be useful to be able to close such invoices as they are paid but not in full.

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