With direct flights an issue at the moment you may be interested in the expereince of one lady to find out how it was for her and her family.
My family and I had to do the Egyptair Heathrow-Cairo-Luxor trip in September after our Easyjet flight was cancelled. I was dreading it as travelling with a 2 and 6 year old you just want to get there as soon as possible. The flight ended up being one of the easiest and least tiring ever.
You check in at Heathrow, your hold luggage gets put on the Cairo - Luxor flight without you having to do anything. You are given a boarding pass for the London to Cairo and another for the cairo to Luxor when you check in. The seats are nice and roomy with a personal TV for each passenger with loads of TV and films etc.
On arrival at Cairo, it's so straightforward. You just follow the signs for connecting flights which leads you through Immigration where they stamp your passport, you go through a hand baggage scanner through to the departure lounge where a bus takes you to your connecting flight. On arrival at Luxor just remember that as your flight was not domestic only you will collect your bags from a different carousel to the passengers who have only done the Cairo -Luxor part of the journey, you will be lead through to a carousel in International arrivals where you collect your bags and clear customs.
Usually my husband and I arrive in Luxor drained from the journey and having to keep the children occupied, usually after dragging them out of bed at 4am. This was the first time I ever arrived feeling refreshed, probably because of the time of the flight (early afternoon instead of early morning) and the comfortable seats. Plus you get 2 x 23Kg to check in plus hand luggage. We only had an hours gap between the connecting flights. Go for it!!