I recently had to rename a repo on my Github account. Github has made this very easy but it's just one side of the issue. Obviously you must also update any references to this remote in other clones, otherwise pushes, fetches etc won't work anymore.
You can do this in two ways:
- open .git/config and modify the url for the remote manually
- git remote rm origin && git remote add origin email@example.com:$user/$project.git
That's it! All will work fine again.