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the 2 week train tour starting in Zurich then to Appenzell

Has anyone ever done this backwards heading to Bern first

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If you're looking at this itinerary plan(https://www.ricksteves.com/europe/switzerland/itinerary), it should make no difference which way you travel around that loop. Scenery and scheduling are similar in both directions.

However, if you plan to take the Gotthard Panorama Express, note those schedule details at https://www.sbb.ch/en/leisure-holidays/travel-in-switzerland/panoramareisen/gotthard-panorama-express.html. It has sometimes not run on Mondays, or not to/from the Lugano stop on weekends. The 2020 version of that schedule is not yet online.