Chamonix to Milan mid September

Your only options are to look at the train schedule to see if it is better than the Flixbus one on that day or rent a car.

5 1/4 hours by train departing at 9:28 am. 3 changes, Vallorcine, Martigny, and Visp.
www.sbb.ch/en

There are other bus companies doing the same route. There are also buses just to the other side, to Courmayeur or Aosta, from where you can continue to Milano.

But the route via Martigny is very nice.

The bus through the tunnel to Aosta and then bus/train to Milan seems the most
direct, but is subject to delays going through the tunnel, which could mess
up the train connection.

You could take a bus back to Geneva and then there are direct trains to Milan
@ 7:39am, 1:39pm, and 6:39pm.

Not an optimal situation. Maybe consider going back to Geneva the night before
and then 4 hr train to Milan early in the morning?

I had Flixbus booked the other way (Milan to Chamonix) for Sept 24 and Flixbus cancelled my trip altogether. I saw that routes were available the next day, so we are overnighting in Milan, then taking the Flixbus early the next morning. Maybe check the days before and after and see if there's a better schedule available on another day? You might also look at BlaBlaBus. I ended up going with them for our Chamonix to Lyon leg, as Flixbus only offered a crazy multi-stop schedule.

Good luck!

I would just take the train. You have to understand that Flixbus is bargain basement prices, and thus also bargain basement service. Flixbus is for people for whom price trumps everything. Even actually getting to your destination it would appear.

I'm not sure I would single Flixbus out vs other bus companies. In general, bus
transportation is a common way of getting around many European countries,
and while Flixbus is definitely an inexpensive mode of transport, I have found
the coaches to be comfortable, the drivers competent, and more or less on time.
And I've found their customer service to be good. Yes, they may have cancelled
the trip you wanted, but they did let you know ahead of time. The fact that there are
few good alternatives was always the situation.

BlaBlaBus does not have a good option, and the train option has 3 changes (good
news is you have time between them). I'd still consider bus back to Geneva and
then direct train to Milan from there.

You can also take the train from Chamonix to Geneva with one change. We are staying in the area and have made 2 trips to Chamonix this week. There is a train every hour (55 before) with one change. The trick of booking a ticket for us has been to book trains on the SBB, Swiss site rather than the SNCF, French site no matter which direction you are going. Staying for one night in Geneva could add enough cost to make the long bus ride look not so bad after all.

If you booked the backwards train trip all in one day, to avoid the expense of a hotel in Geneva and avoid the long bus ride, it would be 9hours, still not good.
Chamonix 8:55 - GVA 11:27
Geneva 1:39-5:43 Milan

But why would you do that when you can shortcut Geneva altogether by leaving at 12:28 pm to Vallorcine, connect to Martigny, then connect to Sion and catch that same train coming from Geneva there that continues on to Milano Centrale. Total travel time is 5 1/4 hours. The connection at Vallorcine is trivial as the connecting train is waiting for your there at the station.

There is also a connection at 11:28 am, but the 3rd connection is in Brig. Same travel time.

I only mentioned the train backtracking because shoeflyer said take a bus to Geneva from Chamonix and I wanted to let people know that there is a train option too. People are often asking about the bus, bus-train, all train route from Chamonix to Geneva. I think one of the RS tours must end in Chamonix and the transportation question comes up a lot.

Personally I wouldn’t be very happy with the Flixbus change but would probably stick with that rather than take any of these alternate train options we’re discussing.

There definitely is the train option Chamonix <-> Geneva, but it involves 2 changes
along the way as the rail gauge changes as you go into the mountains, so it takes
a lot longer than a bus does. It's pretty scenic, but if the train is crowded/you have
a lot of bags, the 2 changes is a negative.

At the same time, the bus station and train station in downtown Geneva are a few
blocks apart. So if you did this, going to the airport might be easier. The airport
train station never seems to be that crowded vs Cornavin downtown.

I understand what Sam is saying about going via Vallorcine, but just am pointing
out there are options.