If you linked an existing book with an existing GitHub repository, the GitBook and GitHub repositories are likely to be out of sync. This case can also happen if you edited both your book and your GitHub repository in parallel.
Whenever your book's repositories are out of sync, you can access the GitHub section of your book's settings to force either GitBook or GitHub to update to the state of the other.
Be careful though, forcing the synchronization from one source to one destination will completely override the destination's content. Make sure not to lose any content by mistake, and to pick the right synchronization direction.