To reproduce:
1. Create a Monobehaviour Foo with a single int field
2. Create an empty object in the scene and add the Foo behavior to the object
3. Set the components field to 12
4. Create a Prefab from the object
5. Close the Editor
6. Move the Script to a folder outside the project
7. Delete the library folder
8. Open the project in the editor
9. Select the Prefab in the Project view
10. Notice the Inspector says "Prefab is missing script"
11. Copy the Script into the project (and refresh, if autorefresh is disabled)
12. Select the prefab and see the field value

Expected result: The field value is '12'
Actual result: The field value is '0'

Reproducible in: 2018.4.10f1, 2019.2.7f2, 2019.3.0b5, 2020.1.0a6

Note: Reimporting the Prefab will fix the issue