Yes, and in all cases where 2 applications are sharing session data and attempting to control the session in any way, regardless of whether one is CI, you will be faced with the same issues. A careful developer with an understanding of how both applications access and manage sessions can make them do so if they're on the same domain, but there are so many potential problems with doing so that it shouldn't be recommended. In most cases it would be better to use different sessions in each application to store a value (like a user id) that can be used to lookup the necessary data in another storage mechanism (database, filesystem, etc.).
