This is not a huge bug as duplicating Assets outside of the Editor in this way isn't the ideal workflow. But there is a customer with this workflow and it causes issues when there are childAssets

To reproduce:

1. Download attached project “2018MetaChange.zip" and open in Unity
2. Open "2018MetaChange" folder and then "Assets" folder
3. Find "New Material" and "DataRoot" assets
4. Duplicate them outside of the Editor without .meta files
5. Focus on Unity Editor and wait while it imports newly created files
6. Look at DataRoot<copy> in the Editor
7. Observe that the DataRoot Object may not be DataRoot - still named DataRoot in Project view
8. Check the previous step by expanding the Object and see if a Child object is named DataRoot (this is the actual DataRoot)
9. Come back to "2018MetaChange" folder and then "Assets" folder
10. Find "New Material<copy>" and "DataRoot<copy>" assets .meta files
11. Open them with Notepad++ or TextEdit
12. Look at the text of the metadata and observe that m_MainObjectFileId have 0 value

Notes:
- This issue appears on both Windows and macOS
- Before Importing newly created assets to Unity Editor, make sure that their name ends with .asset or .mat

Reproduced on Unity 2017.4.0f1, 2017.4.18f1, 2018.2.20f1, 2018.3.2f1 and 2019.1.0a14