Are you able to refund the Application fee for a submitted application?
If the transaction has been processed, you will need to partner with your Payment Gateway in order to refund this transaction. However, in onBoard, you can get the Transaction Id to present to the gateway so that they know which transaction to reverse.
Go to onBoard:
Then select Reconcile Fees
Click Edit on the fee for the submitted application
Scroll down and under Payment Information you will see the Transaction Id field