Agree completely with Camile. Dead roots are not helping the orchid any. And they might be little bacterial sponges harboring wee beasties that may promote rot elsewhere. But be sure they're really dead roots and not just stained brown from poorly pre-soaked potting media. If dead they will feel squishy or hollow or papery or wrinkled and desiccated. With a gentle tug the sheath of the root will often slide away from the stringy core. If they are black or jelly-like or smell like dead things. All signs of dead roots. If, however, they still feel firm to the touch... like a fresh green bean, they're not shriveled and the sheath does not easily pull away from the wiry core - then they may just be stained brown. If dead, do carefully cut them away with properly sterile tools. If alive do not cut! The live roots are keeping the plant fed and hydrated. Do pot into the smallest pot possible given the size of the remaining live root mass. Good luck.
-J
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