BR2 Import and Overwrite Functionality is now working!
To use it first export your a rigged model from Blender via the .br2 script. I would recommend exporting from Blender 2.7x even if you are working in Blender 2.49 as Blender 2.7x exports binormals and tangents for vertices which should make for smoother looking meshes.
Then you have two options:
1) Use "Open BR2" to load both skeleton and mesh data from the .br2 file.
2) Make a copy of the vanilla .fgx model that you have used for your base and use "Open" to open it. Now you can use "Ovwr. BR2" to just overwrite the meshes with the mesh data from your .br2 file leaving skeleton untouched.
After you do either of these you should immediately use "Save" to save the .fgx for stability reasons.
At the moment Material support is minimal. Materials can be renamed but not added deleted. Since the default Materials are take from the Hoplite Armor the tool may only work for Units right now. Hopefully through a combination of renaming Materials here and working with the .ast and .mtl files it will be possible to cook units with both custom meshes and textures that use the vanilla Civ 6 animations.
3D Graphics Tool for Civilization 6