I think the damage done to the railway was as a result of the portal storms that occur after the Citadel's demise. Obviously when you see the first portal storm in the game, it has a pretty profound effect on the already damaged bridge.
My guess: the Citadel collapses during the escape. The train continues onward for a decent distance (and not going directly straight, obviously), before being hit by one of the portal storms, causing the bridge to partially collapse, sending the train plunging into the ravine.