How to reproduce:
1. Open the project from the attached file "1217930.zip"
2. Create a new shape by going to ProBuilder window picking "New Shape"
3. Select the newly created "Cube" GameObject and press CTRL + D
4. Select "Object Selection" tool at the top of the scene view and move the duplicated GameObject so that both GameObjects are visible
5. Pick the "Face Selection" tool at the top of the scene view, press on the top face of the duplicated cube and drag it up
6. Select the non-duplicated Cube GameObject, enter Playmode and inspect the scene view

Expected behavior: The duplicated GameObject has the same shape as before entering play mode
Actual behavior: The duplicated GameObject is reverted to the same shape as the source GameObject

Reproducible with: ProBuilder 4.3.0-preview.2(2018.4.0f1, 2019.1.14f1, 2019.2.21f1, 2019.3.1f1, 2020.1.0a23)
Not reproducible with: ProBuilder 2.9.8f3(2017.4.37f1), ProBuilder 4.3.0-preview.1(2018.4.17f1, 2019.1.14f1, 2019.2.21f1, 2019.3.1f1, 2020.1.0a23)
Could not test with: ProBuilder 4.3.0-preview.2(2017.4.37f1) version not introduced

Note: When selecting the duplicated GameObject made changes are visible as expected. Also reproducible when duplicating the GameObject with the "Mirror Objects" option in the ProBuilder window.