I am making a lowpoly ship for an rts game but i might have screwed up, the model was in different parts, and so it was best to bake textures on them separately, but now it seems i cant merge the texture through baking, it does not seem to work when the textures are from different materials. anyone know how to solve this? i have read around but found no solution. could one manually get them into the same materal but different uv layers somehow? i tried but i could figure out how. I have uploaded the blendfile if anyone wants look at it. In layer 1 is the model with multimaterial, in layer 2 is the attempted merge.
http://dl.dropbox.com/u/5302413/Behemothoriginal.blend