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Train or bus between Marigny and Annecy

We will be traveling to Chamonix from Switzerland in October by train. I understand that they will be working on the rail line during that time and they are using the bus instead. Also, as we will staying in Chamonix for 2 nights we will be eligible for the guest card that covers the train and bus. My first question is that as we will not have arrived at our accommodations in Chamonix yet, is there somewhere we can get that guest card to cover our inbound journey if we can show a confirmed reservation? Also the train and bus schedule is so confusing. Do we need to catch the train from Martigny to Vallorcine to catch the bus, I guess bus not train because of the work being done? When we are leaving Chamonix, we will be heading towards Paris as that is where we are leaving for Canada from. So we plan to train or bus to Annecy first to pick up the high speed train to Lyon where we plan to spend the night and then take the train from Lyon to Paris the following day.

My next question is, because the train from Chamonix to Annecy is so slow, we are thinking the bus might be a lot quicker so we are wondering how reliable are the busses that run? Bla Bla Bus that covers that route has very bad reviews in other areas so I am apprehensive to deal with them. We wold like to spend just a couple of hours in Annecy before we pick up the fast train to Lyon so how far is the bus/train station from old Annecy? Could we lock up our luggage at the station while we are there and walk the distance to town? Has anyone out there done this route and if so, could offer some advise? Appreciate all the help I can get. Thanks from Canada.

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Can't help about the works between Martigny and Chamonix. There's probably no way to use a guest card before you are an actual guest, so it won't help you on arrival day, by the way.
I do not really like the idea of travelling from Chamonix to Lyon via Annecy, then to Paris, just for one night in in Lyon. They may be private luggage storage services in Annecy (look at Nanny Bag for example?), but it's still a hassle, and you won't have time to visit Lyon. How about spending the night in Annecy instead?