How to reproduce:
1. Open the attached project "case_1333408-ApplyToPrefab"
2. Open SampleScene
3. Click on Point Light in the Scene Hierarchy
4. In the Inspector under Shadows dropdown change the resolution
5. Right-click the resolution label
6. Observe the displayed choices

Expected result: There is an Apply to Prefab choice
Actual result: There is no Apply to Prefab choice

Reproducible with: 7.1.1 (2020.1.0a12), 10.4.0 (2020.3.7f1), 11.0.0 (2021.1.6f1), 12.0.0 (2021.2.0a16)
Not reproducible with: 7.0.1 - 7.6.0 (2019.3.0b1 - 2019.4.26f1), 7.0.1 (2020.1.0a1)

Workaround: Change the Resolution dropdown from Custom to something else and then change it back to Custom

Note:
1. This is also reproducible with the Contact Shadow Enable property