Steps to reproduce:
1. Open the attached project
2. Click on Menu > TestAB > Create AssetBundles (Map) > 1. All Assets
3. Note that in the directory "Bundles" located in the root of the project, the manifest "bundlea" contains the four assets that belong to it:
Assets:
- Assets/2048tex.jpg
- Assets/SpherePrefab.prefab
- Assets/grass_normal.png
- Assets/TestMaterial.mat
4. Click on Menu > TestAB > Create AssetBundles (Map) > 2. Assets removed
5. Note that in the same manifest file for "bundlea" the "Assets:" tag continues showing the four assets, despite having erased two of them:
Assets whose should be removed:
- Assets/2048tex.jpg",
- Assets/TestMaterial.mat",

Actual result: The assets are not removed from the manifest
Expected result: Assets should be removed from the manifest

Reproduced with: 5.5.4p2, 5.6.3f1 , 2017.1.0p3, 2017.2.0b6, 2017.3.0a3