We recommend that you do not make changes to the standard libraries of Flamingo. Instead, save your new and modified materials in User.mlib or custom libraries that you create as new libraries and give special names to (like Boeing_Project.mlib).
The reason for not changing the standard libraries is to be compatible with other users in your organization or your clients. If you change a named material definition in a standard library, when you ship .3DM models that use that modified material to someone else with Flamingo, their rendering will use the standard material definition, rather than the modified definition, and your renderings won't match.
When you ship your models to another person to render, send your custom libraries with the drawings, and tell that person where they need to put them.
This procedure has been automated somewhat by the FlamingoTransport command, which exports the needed materials and bitmaps along with the .3DM file. See the Flamingo Help file for details.