Marked as won't fix due to low priority
If you 'Save All' after renaming an asset after it's creation, without any saves prior, it will appear in the windows explorer's content folder but will not be visible in the editor.
1. Create a new project
2. Create a new blueprint asset of any type
3. Rename the NewBlueprint to anything
4. Select 'Save All' in the content browser
5. It will ask you if you wish to save 'NewBlueprint'
6. Proceed with saving the item
7. Notice that NewBlueprint is not visible
8. Navigate to your Content folder for this project in Windows Explorer (Or Finder on Mac)
9. Notice that NewBlueprint is still there
Result: The asset is there twice, as NewBlueprint and as the new name.
Expected: NewBlueprint should not exist anymore, and should not have been saved in the first place. It is possible that the issue is that the renaming is creating a reference to the old name and leaving it there.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-16437 in the post.