The paradox is resolved because two clocks, each in a different reference frame, measure time at different rates relative to each other, depending on the relative velocities of each reference frame.
For example, if a 50-meter-long train (as measured at rest in the tunnel) travels at 250K meters per second relative to the stationary 50-meter tunnel, then to an observer in the tunnel frame, the train's length would appear to be 50 * sqrt(1-(250K^2 / c^2)) = 27.6 meters, and a 50-meter tunnel would accommodate the train as it passes between simultaneously opening and closing doors.
But to an observer on the train, it would appear that the tunnel rushes past at 250 meters per second, and he would expect that his 50-meter train would not fit into a 27.6-meter tunnel. The doors would be unable to open and close simultaneously without smashing the train. Both observers are making valid observations in their own reference frames.
The key to resolving the paradox may be to visualize that travel time can be a measure of distance, and distance travelled can be a measure of time. In order for the on-board observer and the tunnel observer to agree that the train has passed through the tunnel without smashing into the doors, time measured in the train reference frame must differ from time measured in the tunnel reference frame. From the viewpoint of the on-board observer, the tunnel doors do not open and close simultaneously. This provides time for the rear of the train to enter the tunnel after the front of the train has exited the tunnel. But to the tunnel observer, the doors do open and close simultaneously. Both observers make valid and accurate observations, the train does not smash into the doors, and time is the parameter that absorbs and reconciles the paradox.