If a customer invoice was paid in a batch and the payment was later rejected, you can create a refund receipt to "undedposted funds", then select this refund receipt with the batch that the money was "taken back" in. Just be sure to receive the other invoice payments in this batch to undeposited funds as well so the total deposit amount matches what come through the bank feed.  You will make the total deposit on the date it was received, then match it in the bank feed.