We will be traveling from Lauterbrunnen to Munich and would like to do a stopover for a few hours in Zurich. We have a Swiss Pass so our travel in Switzerland should be covered, however we would need to buy a ticket for the travel through Austria and Germany. We would like to take a train passing through the border town of Lindau to get to Munich because I think our travel would then be covered by a Bayern ticket. I have found a EuroCity train which travels from Zurich to Munich via Lindau. However, when I try to find the same train from Lindau to Munich, it doesn't show up as an option on the Bahn.de website, so I'm guessing the train doesn't stop there. Are EC trains covered by a Bayern ticket? How do I purchase the ticket for travel beyond the Swiss Border?
The 9:16 EC train headed directly from Zurich to Munich will stop in Lindau. The DB schedule shows that it departs Lindau at 11:12. But the Bayern ticket excludes high-speed trains like the EC, IC, and ICE trains. You will have to get off in Lindau and take regional trains from there to use the Bayern ticket. To find the eligible regional trains, specify "only local transport" under "means of transport" at the DB itinerary page: http://reiseauskunft.bahn.de/bin/query.exe/en You can use any other train or combination of trains between Zurich and Lindau that you wish, not just the 9:16 train, of course, with your Swiss pass.
You can purchase tickets for travel beyond the Swiss border online from the German Rail (Bahn) website. You would have several options. You could purchase an Europa-Spezial ticket all the way from St. Margrethen to Munich on the EC for as low as €39/p. That's for 92 days in advance. If you purchase closer to travel time, the lowest priced ticket will have sold out, and the price will be higher. You could purchase point-point tickets from St. Margrethen to Lindau for €7,40/p online from the Bahn or for 9,00/p CHF (€7,49) at the counter in Zürich. Then you could purchase a Savings Price ticket for two for the EC from Lindau to Munich. That ticket, depending on how early you bought, it could cost €29 for both of you. If you wanted to go all the way to Munich on the EC, those options would be best. One or the other might be the best choice depending on the price of the tickets at the time you buy them. Lastly, there is an RE leaving Lindau 13 min after the EC and taking 22 min longer, so you would arrive in Munich at 14:04 instead of 13:29. If you knew what you were doing, 13 min would be enough time to jump off in Lindau and buy the Bayern-Ticket. In addition, there is an ALX train leaving Lindau at 11:58, 33 min after the RE, getting into Munich at 14:41. That would give you plenty of time to buy the Bayern-Ticket and maybe take a peek at the Lindau Harbor, which is right outside the Lindau Hbf.
Lee accurately points out that on top of the Swiss pass and the Bayern ticket, you'll need a ticket between the Swiss border and Lindau, a small segment I overlooked in my advice. Sorry for any confusion.
Thank you Lee and Russ for your very helpful information. We are planning on leaving early from Lauterbrunnen and would like to spend several hours in either Bern or Zurich on the way to Munich. The train we are considering is much later in the day, departing Zurich at 18:16 direct to Munich with the border crossings at St. Margrethen & Lindau. With your advice, I am going to purchase the ticket from St. Margrethen to Munich using the bahn.de website in advance, as you both have suggested. The EC train we are looking at is only 39 Euros for two people, which is the same or close to the cost of a Bayern pass with the addition of the short segment through Austria. I didn't remember the regional train restrictions on the Bayern Pass, so thanks for the reminder. Happy travels to you both.