if you're using the official examples (Procedural), have a look at the "Sculpt Vertices" scene (in particular the "PaintVertices" script. From the looks of it, you have to reapply the new mesh to the mesh collider component for it to update that as well.
How do I persuade unity to recognise that a mesh has changed shape? basically I'm trying to stick a box to the surface of a rippling plane I've stolen the example code for deforming a mesh according to a sine wave but seem to be unable to get a raycast from the box to recognise the changing shape of the plane I'm…