Transaction fees are not dependent on if a merchant collects the funds for an order. They are based on an order being placed, the amount of the order, and the status of the order (OK, On Hold, Pending Review). Transaction fees are calculated against the total revenue excluding shipping and handling charges and any applicable taxes, of all transactions conducted through your store.
The monthly transaction fee varies according to the plan to which you're subscribing (currently 1.5% for Merchant Starter, 1.0% for Merchant Standard, and .75% for Merchant Professional) and is due on the 6th day of the month after the calendar month to which the transaction fee applies.
Transaction fees don't apply to canceled, returned, or fraudulent orders. If an order is not marked Canceled, Fraudulent, or Returned until the next calendar month, the transaction fees will still be charged as a part of the billing for the month in which the order was placed.
After an order has been placed, merchants have 90 days to mark an order as Canceled, Returned, or Fraudulent in order to receive an adjustment credit for transaction fees. The credit will occur as a part of the next monthly transaction fee billing cycle for which there is a positive transaction fee balance to issue the credit against.