How to reproduce:
1. Open the attached "ProBuilder Merge Issues" project
2. Open the "SampleScene" Scene from Assets > Scenes folder
3. Select "Cube" and "Cube (Flipped Normals)" GameObjects from the Hierarchy window
4. Merge Objects by clicking Tools > ProBuilder > Object > Merge Objects
5. Select a face of the resulting cube and move it around with the Face Selection tool
6. Click Tools > ProBuilder > Repair > Rebuild Shared Indexes cache
7. Repeat step 5

Expected result: the object doesn't need repairing upon creation and the behavior is identical before and after repairing
Actual result: the object created after merging is instantly susceptible to repairing

Reproducible with: 3.0.0 (2018.4.26f1), 3.10.1 (2018.4.26f1), 4.0.2 (2020.2.0a21), 4.3.1 (2020.2.0a21), 4.4.0 (2018.4.26f1, 2019.4.9f1, 2020.1.3f1, 2020.2.0a21)

Notes:
-In step 3 the cubes are identical apart from normals but that doesn't affect the reproduction of this issue, normals are flipped only for demonstration purposes