Reproduction steps:
1. Open project attached (AssetBundleUpdate.zip)
2. See that all 4 assets are included in AssetBundle "bundlea".
3. Build them by using Menu/TestAB/Create Asset Bundle(Tags).
4. Remove "2048text" and "TestMaterial" from asset bundle.
5. Repeat step 3.

Result: Bundle manifest information is the same.

6. Remove "SpherePrefab" from the bundle.
7. Repeat step 3.
8. Add "SpherePrefab" back to bundle and repeat step 3.

Expected result: Manifest information will be identical the one that we got after Step 5.
Actual result: They are different and after step 8 there is no information about "2048text" and "TestMaterial".

Notes: Adding "2048text" and "TestMaterial" to asset bundle will still provide the same behavior that we have after step 8.

Reproduced on: 5.5.0f3, 2017.1.0p5, 2017.3.0a6.