After our 12 day My Way: Alpine Tour we will be trying to get to Berlin from Chamonix. I have tried google searches for trains, buses, or rental cars, with no success. If anyone has done a similar route I'd love to hear your experience.
Chamonix is well connected to Geneva by bus. You could try flying out of Geneva’s airport or training out of Cornavin (main train station). Both the airport & near the train station were stops on Flix Bus.
Its a 12+ hour train journey with many train changes. I think I would look at a bus to Geneva airport, fly nonstop to Berlin, and a train into the city. Swiss has a direct flight at 6:30 pm, and Easy Jet has morning flights.