Then it isn’t getting to Monzo and you need to ask the merchant.
BUT
If you have a credit card, use that. Monzo Flex isn’t ideal in this scenario. A credit card won’t charge you for a pending charge, Monzo will. So you could end up having to make that first payment and then wait for it to be refunded.
(I know this is for the deposit, not the payment, but it’ll be the same credit card acceptance system employed by EconomyBookings I’m sure)
So on the surface of it, it should work. But Flex can be funny sometimes. It’ll be either Flex being funny or a possible ghost in your machine. One painless non-Flex thing to try: