The way to deal with this is to have a “merchant” bank account in QuickFile to represent your PayPal account. When you’re paid by PayPal for an invoice you mark the invoice as paid in full into your PayPal merchant account, you tag the money you actually received in your current account as a bank transfer from the PayPal merchant account, and this leaves the fee as a residual balance in the PayPal account which you can clear by creating a “purchase” for the amount of the fee and marking that as paid from the same merchant account.
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