Was ZRH cheaper and you wanted GVA via hidden city ticketing? Not sure this all adds up for me with such a short layover and the inevitable delays out of LIS. If you book a broken fare LIS-GVA and GVA-ZRH then you can expect to be routed via GVA, else it is a LIS-ZRH ticket. The best for a stop in GVA would be to book LIS-GVA/ZHT-ZLP - the latter would allow you to take any SBB train the same or the next day.