Reproduction steps:
1. Open the attached project "case_1239258-Animation_Bug.zip"
2. In the Project window under "Assets/Scenes" open "AnimationOverrideBug.unity"
3. Enter Play Mode
4. Press the "x" button on the keyboard to rotate the cube
5. Press the '1' key on the top of the alphanumeric keyboard to replace the clip by itself
6. Repeat step 4

Expected result: animated object's transforms are not overridden by the Update() function when Animation clip is replaced by itself
Actual result: animated object's transforms are overridden by the Update() function when Animation clip is replaced by itself (See attached AnimationOverrideUpdate.mp4)

Reproduces on: 2018.4.23f1, 2019.3.15f1, 2020.1.0b10, 2020.2.0a12