Since trains move in a 3D environment, waypoints are also 3D coordinates. There is however a replace stop tool, located on the special construction tools menu in pak64. Click on one tile and then another, and all vehicles/lines stopping at the first tile will get their waypoints moved to the second tile. Since trains can have their waypoints on any tile along a platform, you may have to do this for every tile to be sure. I have never used the tool for moving lines underground, so I can't rule out that switching between above and underground disrupts the the tool.