Steps to reproduce:
1. Open the provided project "AddressablesSceneUpdate.zip"
2. In the Addressables Groups window select Build > New Build > Default Build Script
3. Enter Play Mode, Press "Load Next Scene" and "Spawn object" buttons
4. Exit Play Mode and make changes to the "NextScene" Scene (e.g disable "Text" GameObject)
5. In the Project window open "Cube" Prefab and make changes to it (e.g increase the scale of the x-axis)
6. Open "SampleScene" Scene, select Build > New Build > Default Build Script
7. Enter Play Mode -> Press "Load Next Scene" and "Spawn object" buttons

Expected results: Scene changes can be seen in Play Mode when Addressable content is built
Actual results: only Prefab changes can be seen in Play Mode when Addressable content is built

Reproducible with: Addresssables 1.1.7 (2019.3.0a5), Addressables 1.1.7 (2019.3.0b11), Addressables 1.1.7 (2020.1.0a13)
Not reproducible with: Addressables 1.1.5 (2019.2.13f1), Addressables 1.1.5 (2019.3.0a5), Addressables 1.1.5 (2019.3.0b11), Addressables 1.1.5 (2020.1.0a13)
Could not test with 2018.4.13f1 and below 2019.3.0a5 due to package related errors

Note: Scene changes can be seen but only if Build -> Clean Build -> All is used in the Addressables Groups window