Simply changing the cliff levels in the cliff mesh data causes big black gaps to appear where the cliff faces separate from the rest of the terrain. This utility fixes that, assuming you have extracted all the meshes for a type of cliff, such as CliffNormal0. Be sure to scale the cliff mesh levels in the data editor by the same amount you scale the models.
Source code (Visual Basic 6) and executable are both available for download.
Problem scenario example:
In order to make, for example, a 1.5x scaled cliff of level 3 connect smoothly with an ordinary cliff of level 2, make the level-2 height of the modified cliff match that of the normal cliff (by default, 2.0). Add (1.5 scale x 2.0 default height = 3.0) plus the level-2 height of the modified cliff, and set this value to the level-3 height of the modified cliff.
Initial commit. (This code is Visual Basic 6.)