I also had to deal with this issue for a customer’s site, and found a way to fix it.
The second subtraction happens in line 118 of the file woocommerce-gateway-paypal-express-checkout/includes/class-wc-gateway-ppec-checkout-handler.php, it has the $order->reduce_order_stock() command, which executes right after the note with the transaction ID is generated, commenting it out is all it takes to solve the issue in the meantime.
