What would happen and how will this be dealt with if the lines were active and in current use at the time of the event?
All transportation modes are subject to impacts from tornadoes and hurricanes. Fortunately transportation deaths such events are very rare compared to common accidents. Higher speed ET3 will be underground this will also help mitigate wind damage risks.
If an unlikely tube ruptures occurs, sensors activate a safety routine to reduce risks. The damaged section is isolated with gate valves, traffic rerouted, and then air is admitted all along the tube via apertures sized and spaced such that the rate of capsule deceleration is high yet survivable. The air between the capsules reduces the likelihood of collisions as they slow down and encounter the inrush of air from the rupture.