Steps to reproduce:
1. Open the attached project
2. Open "empty scene"
3. Notice that the "Shotgun" prefab already has an override (if it doesn't, just hover over scene view)
4. Select the "Shotgun" prefab instance
5. In the Inspector window click on Overrides dropdown
Expected result: No overrides
Actual result: Prefab child GO has updated rotation
Reproducible with: 2019.4.34f1, 2020.3.28f1, 2021.2.10f1, 2022.1.0b6, 2022.2.0a4
Notes:
- The updated rotation comes from the randomReference.cs script which just calls Handles.Rotation in OnDrawGizmos(). This shouldn't alter rotation as the call returns the same value as the current one
- Tried reproducing with built in GameObjects, but couldn't
- More info and an alternate scenario can be found in the edits