I prefer to change all links, including project names, folders, namespaces, everything when the real name changes. It may be a little painful, but it is better in the long run, especially when new developers are introduced to the project and are not familiar with the story.
Some companies continue to use code names within the company even after the real name is determined and released. Even today, there are places where "Opus" appears in connection with Microsoft Word (when information about the window handle is being digged, and not any published api or ui).
If you keep the code names around, you get a mess and a large document to know what's what.
http://en.wikipedia.org/wiki/List_of_Microsoft_codenames
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