Steps to reproduce:
1. Download and open the attached project
2. Open Assets/Data/TestObject in the inspector to observe changes
3. Go to Assets-->Modify asset (this adds a "!" to Element 0 of TestObject)
4. Save the project (this does nothing)
5. Close the project
6. Open the project

Expected result: TestObject has the modified value
Actual result: TestObject has the value from before being modified

Reproduced on 5.2.3f1. 5.3.7p2, 5.4.3p3, 5.5.0p1, 5.6.0a5

Notes:
-modifying the object manually by inputting values into it's elements is registered normally
-one consequence of this is AssetBundles not rebuilding the asset modified through the script(original submitted issue)