Here an example with icecraft and a part of another map:

The idea behind this is that once a map is finished with all the objects like trees and houses in it, you could simply export the colormap from it and use it as a layer in gimp/paint.net. this way things like shadows can be added to the old colormap which was initially used to create the map without any objects. Now with a script like this it would be possible to simply overlay the old, unshaded terrain with a new shaded one without destroying any structures.
This is already possible in Qubicle, but unfortunately Qubicle hollows any structure like trees or arches out and it can take hours to refill those objects given the limited speed at which Qubicle handles large files and its proneness to crash.