When re-importing an OBJ into blender, there is no material replacement. Blender won't assume either the materials in the .blend nor the ones in the .obj . So what does it do? It creates duplicates in the form of materialname.001 . BlenderArtists.org forum user Alain has devised a clever modified OBJ import Add-on to circumvent this problem. It was posted originally in BlenderArtists.org forums here, but for the sake of being sure this precious file doesn't disappear from the face of the internet, we are keeping a copy in our very own blog. Get it here.
February 27 2013