When upgrading a project from Unity 4 to Unity 5, you may need to re-bake stored data because some of the prebaked data formats have changed.
Baked Occlusion Culling data format was changed. Rebaking is required for the occlusion culling data.
Baked Lighting data format was changed. Rebaking is required for the lighting data.
Is something described here not working as you expect it to? It might be a Known Issue. Please check with the Issue Tracker at issuetracker.unity3d.com.