Reproduction steps:

# Open the “proBuilder” project
# Open the “SampleScene” scene
# In the Hierarchy select the “Test” GameObject
# At the top of the Inspector locate and click on the “Overrides” button
# In the Overrides window press “Apply All”
# 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