This is still an issue and unfortunately neither PayPal or Intuit Quickbooks online will help in anyway what so ever with the issue.  Quickbooks support told me to contact PayPal, and PayPal said this is an issue both partiers are working on (then sent a link here) and immediate closed my support ticket.

I tried to talk with Quickbooks support 2 times and asked 2 people if there is a way manually add the refund but both support techs completely refused to help in any way at all and said I need to contact PayPal.

I am looking for advice, should I keep trying to find a way to add a refund in Quickbooks or should I give up and remove PayPal from Quickbooks online as there is no way for me to accurately make my PayPal in Quickbooks match my actual PayPal account?