There is one iron rule in editing with GWX SH4TerrainEX. It should be written in red letters - Never edit already redone squares!!!
This will lead to what you wrote about. However, this is also fixable. It just takes a little fiddling around.
But never edit what has been changed. The best way out is to redo the square
yourself or apply the converted square to the native one and convert it. But I wouldn't risk it. Taking the square out of the game, we are already violating its integrity. If you do this many times, then voids appear. I call them Wandering Pixels. That's why I never use the same square twice.
