Alot of time lets say i modified a character hair clothig to Matte ect, after meging them to another scene all their materials go back to glossy or sometimes materials in the scene that I imprted them into goes out of whack. Its happened quite a bit.. Been working in duf format for quite a while. Also materials like LIE makeup and such did not need to have any special modidcations to work before 4.5 like this render using LIE makeup but now you have to do what Anton suggested a few times or collect textures I believe http://fav.me/d539jsr