In the event that you have to process refunds after 60 days you will need to download the mass pay file sheet in PayPal. The affiliate will be notified to expect a payment. So, you will need to contact them letting them know that they won't receive the commission since it was refunded but it doesn't show in JVZoo because the requirement of a refund lies within the 60 days.
Since the Paypal refund period is only 60 days JVZoo cannot manage refunds outside of 60 days. You can pay delayed payments up to 90 days, however once an affiliate payment is made the system can only track refunds for 60 days as that is the refund period in Paypal.
As previously stated, you will need to contact the affiliate directly if you wish to obtain any refund from the affiliate. This has always been the case with bank charge-backs and now includes Paypal's longer dispute period.