If you somehow miss the guaranteed connection, Amtrak will either use a bus to catch you up to the train later down the route or put you up in a hotel until the next train comes through (and if that train is sold out of sleepers, they will downgrade you to coach). If they think you are likely to miss the connection, they may take you off the first train early in hopes that a bus can make up the time and get you onto the second train at the original transfer station. They are not going to fly you.