Some types of payments are set up to not get a receipt and not get a reciept number. When attempting to apply a negative payment these payments don't show up in the apply screen as they don't have receipt numbers.
Per phone tech support I temporarily added a receipt number to a payment I needed to reverse and deleted it afterwards.
It would be better if all payments showed up in the apply screen, regardless of receipt whether or not they had a number.
Thank you for considering this.
All the best.