Well a pic would help because it can depend, but usually you have to delete those faces because they can't be helped. Use the append to polygon tool to reinsert those faces and remember to save multiple copies of your file so that you can fall back on an earlier version if something gets screwed up.
"The reasonable man adapts himself to the world; the unreasonable one persists in trying to adapt the world to himself. Therefore all progress depends on the unreasonable man."
George Bernard Shaw - Man and Superman