Anyone who as used Artlantis as main render engine for ArchiCAD models knows how straightforward it is to update new geometry.
The problem lies in Blender's way of dealing with material entities. When a mesh is imported, Blender change it's material name to "material.001" in case there is already a "material" in the scene, so nothing gets overwritten.
Blender Artist's forum user Alain has modified the native OBJ importer script so it has an option for imported mesh's to adopt existing materials. This modified script was posted in this forum thread, and you can download directly the modified script from here.
After downloading, you have to replace the folder of the same name inside Blender's folder / package.