What you do Derek is raise an invoice to the full amount before discount.
Presuming they pay it within the time limit and have deducted the amount they were entitled to, you simply raise a credit note for the difference and send it back to them.
This balances the books of both parties involved
So for example..... you charge me £100 but 10% discount if paid within a week. You send me the invoice for £100, I send you a cheque for £90, you send me a credit note for £10)
Simples