Steps to reproduce:
1. Open Project "MaterialReferenceBug"
2. Select GameObject Prefab in the Assets Folder
3. Open "Sini" Tab in the Top Menu Bar and press "Check Reference and Renderer"
4. Check the Console and take note of the Material ID
5. Select GameObject in the Scene Hierarchy
6. Open "Sini" Tab in the Top Menu Bar and press "Check Reference and Renderer"
7. Check the Console and take note of the Material ID, it matches the previous ID
8. Select GameObject Prefab in the Assets Folder and press Open Prefab
9. Material ID is different and Path is no longer defined

Expected results: Material ID is referenced consistently in Prefab Mode, Scene Hierarchy and Assets Folder for the same GameObject, the Path is defined
Actual results: Material ID in the Prefab Mode is referenced differently from the ID in Scene Hierarchy and Assets Folder, the Path is no longer defined

Reproducible with: 2018.3.5f1, 2019.1.0b3, 2019.2.0a5

Note: Improved Prefabs were introduced in 2018.3.0a6

Update: fixed in 2018.3.10f1, 2019.1.0b6, 2019.2.0a7