Reproduction steps:
1. Open the attached project;
2. Open the Controler in the Animator window;
3. Observe that Layer2 is synced layer of Layer1;
4. Observe that State1 has a blend tree with animation clip ClipA;
5. Select Layer2, then copy State1 and paste it;
6. Select Layer1 and double click on the State1 0;
7. Drag a new clip to the blend tree to replace Clip A (Clip B has been provided in the asset file “WalkLeft”);
8. Select Layer1 and double click on State1 to open the blend tree;
9. Observe that the animation clip change to Clip B.

Expected results: All changes made on synced layer should stay only on this layer.
Actual results: Changes made on synced layer reflect Base layer and States are linked on this layer.

Reproduced on: 5.4.4p3, 5.5.2p2, 5.6.0f1, 2017.1.0a3.