Reproduction steps:
1. Create and open a new project (or use the attached);
2. Change the default light from Directional to Area (baked only), change its color (ex: blue).
3. In Lighting window, click on Generate Lighting -> notice the Lightmap created, with blue faces of your cube visible.
4. In Project window, duplicate the scene (ctrl+D)
5. In the new scene, change the color of the light (ex: red).
6. In Lighting window, click on Generate Lighting -> notice the Lightmap created, with red faces of your cube visible.
7. Open the first scene -> notice your lightmap has disappeared.

Expected results: both scenes will have their specific lightmaps.
Actual results: the original first scene lightmap disappears after baking the second one.

Reproduced on: 5.5.3p3, 5.6.1f1, 2017.1.0p2, 2017.2.0b5, 2017.3.0a2.