Paris to Chamonix drive...suggested overnights? And - returning car to French side of Geneva Airport

As to the rental return at Geneva French side -- we've picked up and returned cars there. On returning, we approached from Ferney-Voltaire, and I don't remember it being terribly confusing. Maybe I was well-prepared. In any event, here's a link to a road map from the airport's web site which shows includes routes to access the French side.
http://www.gva.ch/en/Portaldata/1/Resources/fichiers/publications/af.pdf

For a sleep in northern Burgundy that is not too far from Guedelon, perhaps stay in Vezeley. It is stunningly beautiful and very historic.

Are you sure, however, that you want to do quite so much driving? It's only 3 hours or so to Guedelon, so that makes some sightseeing feasible, but it's likely 5+ hours from there to Annecy (plus add stops for meals and perhaps drive-by sightseeing). That does not leave a ton of time before you'll want to leave for Chamonix.

All in all, a lot of time in the car.

I am not saying you cannot do that, only that you might prefer not to. Consider that, on the other hand, a train trip to Lyon would only take 2 hours, and then it's not far (3 hr, maybe?) to Chamonix by car. (And Lyon is a fabulous destination.)

London . . . . , take the Chunnel to Calais, rent a car

Not a good plan. Very few Eurostar trains (please, not "chunnel") stop at Calais (see current timetable here: https://content-static.eurostar.com/documents/UK_timetable.pdf ), and the ones that do, stop at Calais Fréthun, which is outside Calais near the tunnel mouth. They do not stop in the centre of Calais. This is not a good a good place to pick up a rented car.
Much better to get off the train at Lille. Many more trains (see timetable) and many more car rental companies actually at the station. And Lille is worth a few hours visit.

At the end of your trip, I too would suggest returning your car at the French side of Geneva airport, and avoiding having to use a bus from Chamonix.

Plan B: You currently have London - drive Normandy - Caen, return car train to Paris (4 nights no car) - drive Paris to Chamonix (new car).
I would suggest: London - Paris (train, 4 nights). Now pick up your car and drive to Normandy (or train to Caen and pick up car) - drive direct from Normandy to Chamonix avoiding Paris.
Advantages: The miles you save not driving Calais/Lille to Normandy is more than the extra from Caen, and you might save some going direct avoiding Paris. You only have one car to pick up and return, not two. And London to Paris by train is a quick 2h15.

Thank you, all! I'm looking at these possibilities.

I was in Chamonix recently and found it very efficient to take a bus from the Geneva airport there and back. Once in Chamonix you don't need a car; it is a small, walkable town with a good local bus system, and the narrow roads do not make for easy driving. I'd return the car to Geneva and bus the rest of the trip. Geneva-to-Chamonix buses do require advance reservations. Check AlpyBus for one option.

Thank you for your replies. I have made some changes to the later part of our itinerary. As for the Eurostar, unfortunately I had already booked the tickets. I am unable to change the destination to Lille (can only change time or date) and I have been unsuccessful in booking an additional leg from Calais Frethun to Lille. I'll call them and see if there's anything to be done but I am not optimist. I did find information that indicates that there is some sort of transportation that connects Calais-Frethun and Calais-Ville, as well as Calais Frethun to the port.

Here's the information, from this website http://www.calais-guide.co.uk/trains-taxis-and-buses-in-calais.html
"Calais has two stations: Calais-Ville in the centre of Calais and Calais-Fréthun (for TGV and Eurostar) located southwest of town near the Channel Tunnel entrance. They are connected by the free Navette TER. There is a regular courtesy bus service to and from the station to the port."

There is a europcar office at the port. I may have to go that route if I can't fix the train ticket issue.

Of course, I wish I hadn't been so anxious to get my train tickets...wanting to nab the lower prices, and had done additional research, but it's water under the bridge now and I'll have to punt.

Thanks again, and if anyone has any other suggestions or has information about the Navette TER or courtesy bus. I'm all ears.