Thanks @JoesemM , really appreciate the help.

I've reviewed the details you provided, but unfortunately still do not see any of the refund transactions in my bank feed. I've looked for them as expenses, but they do not appear. I have transfers where I moved money in to my Paypal account to make the refund payments, but do not have the actual refund transactions.

Would you mind further explaining what you meant by if it was included as a lump sum deposit how that might create a problem? I book the transactions as Sales Receipts, if that helps make things more clear. 

Thank you again.