Yes, you are absolutely right about that. Unfortunately, I am not aware of any setting or toggle that can be changed to preserve the edits to the triangles. Since InRoads is feature-based, the triangles are going to be recalculated based on the features. Since the features haven't been edited, you go right back to your original triangles. One workaround would be to import the triangle legs as breaklines and then export the surface. This would retain those flipped triangles.
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