Reproduction steps:

1. Open the “proBuilder” project
2. Open the “SampleScene” scene
3. In the Hierarchy select the “Test” GameObject
4. At the top of the Inspector locate and click on the “Overrides” button
5. In the Overrides window press “Apply All”
6. At the top of the Inspector click on the “Overrides” button

Expected result: No overrides available to GameObject
Actual result: Overrides are still available as if they have not applied

Reproducible with: 5.0.4, 5.0.6 (2020.3.38f1, 2021.3.8f1, 2022.1.14f1, 2022.2.0b6, 2023.1.0a8)

Reproduced on: Windows 10

Note: actual changes are being applied to prefabs but the Overrides in the Inspector stay as if unapplied. Happens only with the ProBuilder related components