[audeyisaacs]

>(I also have the opposite problem when the customers actually pay, because they often batch many invoices together into one payment, which makes reconciliation surprisingly difficult. I wrote a little script in Python to make that easier - sort of along the lines of "Given this total, which of these invoices could potentially satisfy it?" - but it's still frustrating.)

Why not have accounts with client codes? Instruct clients to put their client codes in the narration(they won't always, but most will put something identifying themselves).

Instead of reconciling individual invoices, just sum the invoices of a particular client. If there's still an amount owing, it's for the most recent invoice(s).