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i am exploring 2 options for train routes from Prague to Munich.

One a direct train but with a notice on the website about immigration check and possibility of train disruption.

Another route from Prague to Cheb, a transit time of 9 min to Nuremberg, and another 6 min of transit time to Munich.

Which will be a better option

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With two changes each only a few minutes your risk for delays and missed connections is likely bigger than the risk for delays on your direct train. As indicated in the first answer, you will likely be able to use your same tickets for later trains, but if you buy separate tickets and get under the minimum connection time the railways may deny you that option.

I would go for the direct train unless the train with the connections is much cheaper and fits with your departure time better. And even then I would likely go for the direct train as it is more comfortable to stay in the train.

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This is probably something only you can answer since you know your priorities and your ability to catch trains with tight connections. The phenomenon you describe about the first train has been observed for the German-Polish border https://jonworth.eu/illegal-and-systematic-non-schengen-compliant-border-controls-at-frankfurt-oder-31-august-2022-every-train-controlled-every-train-delayed/ where since both countries are in Schengen it is probably illegal. That does not mean it cannot happen as the Bundespolizei seem oblivious or are perhaps obeying higher authorities.

If the more roundabout route is bookable as a single ticket then in theory if you miss the connection you should be able to get the next train without extra charge but you would have to investigate when the train might be.

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