Coupon applied to Afterpay order but not to WooCommerce order

Customers place an order in the store, uses a Gift Certificate (partial amount of the subtotal), the discount is applied to the cart. Chooses AfterPay as the payment method at checkout, the value still shows the discount. The store confirmation email shows the subtotal less the coupon amount with the correct total.
The customers AfterPay account shows the correct total amount with the correct total for the 4 payments.
However, the Woocommerce order has the coupon applied but no discount amount, therefore a discrepancy with the order total values.
We import our WooCommerce orders into our on-premises ERP (MYOB EXO Business)
This creates a discrepancy between the payment amount in our ERP compared with the AfterPay amount when we reconcile, so we see the customer as owing a debt.

Is this a problem with how the Afterpay plugin writes back to the woocommerce order