How to reproduce:
1. Open the user's attached project
2. Open 'SampleScene' (Scenes > SampleScene)
3. Select File > Save As and save the Scene with a new name
4. Open the previously saved Scene
5. Open Window > Rendering > Lighting
6. In the Lighting window open the Baked Lightmaps tab
7. In the 'Generate Lighting' dropdown select 'Clear Baked Data'
8. Create an empty object in the Hierarchy window
9. Save the Scene
10. Reopen the Scene
11. Observe the Lightmap list in the Lighting window

Expected result: The Lightmap list is empty
Actual result: The Lightmap list has one element

Reproducible with: 2018.4.30f1, 2019.4.16f1, 2020.1.16f1, 2020.2.0b14, 2021.1.0a8

Notes:
- The Scene is not marked as dirty after clearing the baked data