Reproduction steps:
1. Open the attached “ASD” project
2. Open the “Assets/Cube.prefab” Prefab
3. In the Scene View select “Face Selection” button
4. Select a face of the Cube
5. In the top menu select Tools > Probuilder > Actions > Strip All ProBuilder Scripts in Scene
6. Save the prefab
7. Open the “Assets/Sphere.prefab” Prefab
8. Open the “Assets/Cube.prefab” Prefab

Expected result: The Cube GameObject Prefab no longer has the ProBuilder MeshFilter Component
Actual result: The Cube GameObject Prefab is not visible and has no Mesh assigned to it

Reproducible with: 4.5.2 (2020.3.47f1), 5.0.7 (2020.3.47f1, 2021.3.23f1, 2022.2.16f1, 2023.1.0b13, 2023.2.0a11)

Reproducible on: Intel MacOS 13.3

Notes:

* The Cube GameObject is still visible in the SampleScene.unity Scene
* If you select Cube GameObject in the Hierarchy Window, the Inspector Window displays that the GameObject’s ProBuilder MeshFilter component was replaced by Mesh Renderer but still has a Mesh assigned to it.