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Bernina Express to Glacier Express? Bernina Express route question

2 active seniors traveling (flying into Munich by accident) jumping on the train to Garmisch (niece lives there) October 1 for 1 night in Garmisch, we should have a full day to explore around Then, the next afternoon we will train to Chur, stay there 1 night, and catch the BE on the morning of the 3rd. for the start of BE. Does the BE connect with the Glacier Express - do we have to change at Pontresina? We are heading toward Lake Como (Varenna or Menaggio?) and then to Champery, where my other niece lives. Thinking of staying at Varenna or Menaggio (?) for 2 nights, then my niece will pick us up after we train to Montreax. Then 2 nights in Champery. We have to leave Champery for Pisa on Oct. 7. We are traveling by train, pretty exclusively. Really also want to take a ride on a cog train somewhere! Thanks for any insight!

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The Glacier Express travels from Zermatt to St Moritz via Chur. The Bernina Express travels from Chur to Tirano via Samedan (near St Moritz). They overlap between Chur and St. Moritz.
In your case, you will take the Bernina Express only. The named train travels directly from Chur to Tirano, where you connect to Varenna. There are many more regional trains that travel the same route everyday, typically with a connection in St Moritz or two (easy!) connections in Samedan and Pontresina.

By the way, if your niece lives in Champery, you can take the train all the way there if you so desire! From Varenna, head to Milan, and change there for a train to Brig or Martigny. Then Brig/Martigny-Aigle, and Aigle-Champery.