The MT940 files you can download from Mollie are intended to automatically reconcile invoices in your accounting system. Mollie, however, does not have insight in all of your PayPal payments and refunds, only in those received via Mollie. If, for instance, you log in to PayPal and refund or receive a payment, Mollie has no way of knowing about this. That's why we do not include these payments in the MT940 exports.
PayPal itself offers export possibilities to enter the transactions into your bookkeeping.