Repro steps:

1. Open "asset-guid.zip"
2. In File Explorer copy the "Assets\enUS" subdirectory. This will create two assets with the GUID of '5cdfad47a23471445b74de1eaeecf376'
3. Switch back to Unity
4. Notice the warning output in the Console:
"The GUID for Assets/enUS - Copy/VO_...wav is already in use by Assets/enUS/VO_...wav. Assigning a new guid.". (This is correct.)
5. Open up "Assets\enUS\VO_...wav.meta" and "Assets\enUSCopy\VO_...wav.meta" with a text editor and note that the GUID has been changed and they now have different GUIDs.
6. In File Explorer copy the "all-together" folder into the Assets folder. This is a similar situation, there are three assets inside with the same GUID "ac8628a9645a32549a87f20955051199"
7. Switch back to Unity.
8. Notice there is no message about a GUID already in use in the Console
9. Open up "Assets\all-together\test-deDE\VO_...wav.meta", "Assets\all-together\test-enUS\VO_...wav.meta" and "Assets\all-together\test-esES\VO_...wav.meta"
in a text editor and note that all the GUIDs are still the same value "ac8628a9645a32549a87f20955051199"

Expected Result: The three copied assets should be assigned new GUID's/A warning should apear that there are assets with the same GUID
Actual Result: The GUID's are the same as the original files/ No Warning for same GUID's appear if asset isn't in the Assets folder.

Reproduced with: 5.5.4p2, 5.5.0f3, 5.4.5p4, 5.3.8f1
Did not reproduce on: 2017.2.0b3, 2017.1.0f3, 5.6.2p4, 5.6.0p4

Fixed in: 5.6