What I do is look up every sinkhole, go to Topology, set the radius to minimum and then use the "Plateau" function clicking adjacent to the hole to get it on the same level again.
The one in your screenie doesnt show to deep. The "fun" starts when you get them at 100m+ height.
Something that might be worth trying is to create a new one-board route in TS12, and then merge the old route into it, and then save under a new name. Close and then re-open, and see if replace textures still causes the problem.