Unless you and they have agreed a self billing arrangement then yes you’ll need to issue them a credit note, or credit the disocunt against future sales, adjusting the VAT and consideration on those invoices. How are you actually arranging the exchange of money, presumably when they invoiced before you paid, but what are you doing now there’s just a statement? Answering that will probably guide you on how you should proceed.
If they’re knocking it off the money they pay you on future supplies then show it on those invoices, if you’re paying them the money still, then issue them a credit note at the time you pay them. It’s basically whatever you agree between the two of you as to how this rebate should work.