To reproduce:
1. Open attached project "TimelineKilling.zip".
2. Open "Test" scene.
3. Open Game window and Timeline window.
4. Select "Cube_Timeline" object in hierarchy.
5. In Timeline window, select animation clip, to open it in Inspector.
6. In inspector window find "Clip Root Motion Offset" and change any position or rotation value.
7. Press Ctrl+z.

Expected result: Undone action is visible in Scene and Game window.
Actual result: Action is undone, but nothing changes in Scene and Game windows.

Reproducible: 2017.1.0p1, 2017.2.0b4, 2017.3.0a1

Notes:
If Animation was newly added to the Timeline, and Editor was not closed yet, then "Edit->Undo" works (but not the ctrl+z). Ctrl+z works fine with Scene window, but Game window is only updated after mouse enter the Game window.
But after closing the project and reopening it, undoing "Clip Root Motion Offset" does not have any effect in Scene or Game window, until any other object is selected in Hierarchy, or Play button is pressed.