In the editor, fly around the edge of the 'flattened' square. Confirm that it is indeed a single grid tile in game. From the pics you've posted it sure looks like it. If you have a backup of the route, you can replace that specific tile with the backup from your route's Scenery and Terrain folders.
I noticed this exact effect recently when running a test route that I had made years ago. I have no idea why a route tile in a user made route would suddenly get glitchy, or get corrupted like this
