It seems you are modifying the heightfield procedurally. The problem is that the terrain precomputes the chunks average, min and max height to perform efficient culling.
Try calling generate() after you modify the heightfield (I guess in generator.py after line 153 or so).
Right now this will regenerate all chunks (which can get slow depending on your heightfield size), but I think juzzuj made a patch to only update the min/max heights and only update the changed region (not sure if its in yet).