I think the problem has something to do with the cargo packets lost. If you enable the option in the bottom right menu labeled “Cargo”, cargo packets are shown and you can see them moving around to ride trains, etc.
When you do some modifications, specially altering rail tracks, roads, etc., some of these packets are destroyed. Since they don’t reach the intended destination, you’re punished and the working line starts anew.
It may also happen that a working line, with just the same configuration (I don’t know why), won’t recover. If we knew the exact mechanics of supply-demand in the game, we could, as players, do something about it…