Steps to reproduce:

1. Create a new project
2. Create a directory "A" in 'Assets' using the editor
3. Close unity
4. Delete 'Library' folder
5. Copy A.meta
6. Rename 'A.meta copy' as 'B.meta'
7. Create a directory 'B'
8. Open Unity

Expected behaviour: B.meta is updated to use a different GUID than the A.meta (which is exactly what is done when you do the above steps without deleting the Library folder)
Actual behaviour: A.meta and B.meta continues to exist with the same GUIDs