The collapsed bridges, tunnels (not bridge-type tunnels), and sunken roads occurred to a "surprise" code update back in TS12 HF4 that changed the type of assets are classified and further changes were made in a later T:ANE service pack. I remember when this occurred because many of us route builders were quite miffed because we had to go back and fix bridges and roads as well as other splines such as bridge railings. The tunnel type you have encountered, as I said is not a bridge-type tunnel. In Trainz, tunnel track is considered a type of bridge and not track. The other kind of tunnel found on the ECML route and many others is a create your own tunnel using dig-hole assets, spline tunnel walls, track of choice, and separate tunnel entrances.
In the olden days, splines were a different animal and acted differently from track. After this "update", all kinds of annoying issues occurred including this one. When this was done, it changed how the splines interact with the terrain causing them to sink to ground level wherever a spline point is placed just like track does until the track height is set by adjusting the z-axis. Just clicking on the spline point with the adjustment tool will set "lock" the height to that of the other spline points on the same asset.
As always and as it goes here, many routes were affected, and many route-builders were more than annoyed. We were told that the DLC route would be fixed soon(tm) but soon(tm) never came. For a route that someone purchases, this is a glaringly obvious bugger on N3V's nose.