The “underpayment settings” need to be set before the invoice is underpaid.  

Underpayment settings are as follow:

Go to your account settings thereafter select “Settlement settings”

Scroll right down, you will see Underpayments. 

Please ensure you tick in the box provided “Automatically accept invoice underpayments. If left unchecked, underpayments can only be refunded.

Enter your amount percentage and Save.