How to reproduce:
1. Open the attached project "bugExample.zip"
2. Open "SampleScene" Scene
3. Click on "GameObject" GameObject in the Hierarchy window and observe the "X" value in the Inspector window
4. Click on "GameObject" Prefab in the Project window and observe the "X" value in the Inspector window
5. Click on Open Prefab in the Inspector window and observe the "X" value
6. In the Project window, open the "test" script and change "x" value to anything else
7. Repeat steps 2-5

Expected result: old X value remains in the Inspector window but is highlighted, indicating that it's overridden
Actual result: old X value remains in the Inspector window and it is not highlighted, but if the Prefab is opened, the changed value can be seen

Reproducible with: 2018.4.26f1, 2019.4.8f1, 2020.1.2f1, 2020.2.0a20

Notes: To repro on a new project, add an empty script to a GameObject, and create a prefab. Then add a new variable, save the script, change the value of the variable, and save again. This only reproduces if a new variable is introduced to an existing prefab.