How to reproduce:
1. Open the attached project "ShaderSystemIssue.zip"
2. Open the "SampleScene" Scene
3. Enter the Play mode
4. Select the "SCENE MANAGER" GameObject in the Hierarchy window
5. Press the "Swtich Shader" button in the Inspector window
Expected result: The Material of the "Cube" GameObject switches to "Lit"
Actual result: The Material of the "Cube" GameObject becomes transparent
Reproducible with: 2019.4.38f1, 2020.3.33f1, 2021.2.0a21, 2021.2.0b1
Not reproducible with: 2021.2.0b2, 2021.2.19f1, 2021.3.1f1, 2022.1.0a1, 2022.1.0f1, 2022.2.0a11
Note: Selecting the Material in the Inspector window fixes the issue