A lot of train stations no longer offer storage. To know if your travel destination train station does, check http://www.gares-en-mouvement.com/en/. To be absolutely sure (because things change), please check the contact numbers listed on each of your train station’s sites. Some stations are connected to “velo stations” which serve as rental locations and bike parking spaces. For logistical reasons, we’ve used the velo station in Grenoble a number of times to store bikes and bike cases (http://www.metrovelo.fr/) . We’ve also used the velo station in Chambéry (http://www.chambery-metropole.fr/83-velostation.htm).
Depending on the hotel you book, you may be able to leave your bike box in the reception area. Most (but not all) 3-star hotels offer this amenity. 1- and 2-star hotels (Formula 1, Etap, B&B) are reluctant for security/liability reasons. So be sure to your hotels’ official policy on this point.
We can’t speak for other tour operators but, in our case, we will store bike boxes while our guests are on tour. We do our utmost to be accommodating and—although we offer this service for people who don’t buy anything from us—preference is (of course) given to regular clients and clients who buy tours from us. We also know some bike shop managers who offer the service free of charge when you buy an “assembly” service from them (when they assemble and disassemble your bike for you upon your return) and they have space!