How to reproduce:
1. Open the attached project "BugRepro_PrefabGrandchildLosingOverride"
2. Enter the "PrefabChild" prefab
3. Right click on the component "Box Collider" and select "Added Component > Apply to prefab 'PrefabParent'" OR select "Overrides > Apply All to Base" at the top of the Inspector
Expected result: PrefabGrandchild still has "isTrigger" set to true, overriding the "false" value from PrefabChild
Actual result: PrefabGrandchild has "isTrigger" now set to false, like PrefabChild
Reproducible with: 2020.3.44f1, 2021.3.18f1, 2022.2.6f1, 2023.1.0a26
Not reproducible with: 2023.1.0b1, 2023.1.0b4, 2023.2.0a2
Reproduced on: Windows 10 (Intel)