If the 3 step process from the readme file is followed, then NGUI should be completely gone from your project before importing the update. If that's the case, then there is nothing to rename, as all files should already have proper names. If that's not what you are observing, then NGUI does not get removed properly -- and why this happens I cannot tell you. Perhaps it's your versioning system not letting you do it, or maybe you have some files locked, or something else.