Checked with version: 2018.1
When you work with Multi-Scene editing, please make sure that the Lighting Settings of all individual Scenes match the combined Lighting Settings.
Unity creates one single Lighting Data Asset in the Project even when loading multiple Scenes in the Editor. When loading multiple Scenes, the Lighting Data Asset contains one Lighting Data Asset for each Scene. In the Project window, unfold the combined Lighting Data Asset container to see the single Lighting Data Asset that each Scene references.
Even with Multi-Scene editing, the Editor shows one unified set of Lighting Settings, which is a source of potential confusion. Each Scene retains its settings, and the Editor displays only the result of all Scenes merged. Loading each Scene individually in the Editor or Play Mode might show that they have different settings. Changing the order of loading or making another Scene active in Play Mode or Edit Mode can then suddenly cause a diﬀerent overall appearance.
Note: The Lighting Settings also include the Auto Generation setting. Click the Generate Lighting button to trigger a Multi-Scene bake. Unity only loads the result of this bake if the Scene is the actual driver. If an additionally loaded Scene has Auto Generate enabled in its Lighting Settings, it impacts the GI. Loading this Scene individually or setting the Scene active in Play Mode results in all GI vanishing.