Customer paid with a different exchange rate to invoice resulting in a balance on invoice for exchange rate differences. How can this be cleared retrospectively?

Hello

You can do a credit note to clear the difference om the invoice. Or you can do a journal entry(depending on what accounts you are wanting to hit) and attach it to the invoice as payment if you select the debtors and customer name on one of the lines it will point to that customer

Any questions  let us know

Thanks

Emma