To reproduce:
1. Create a new project
2. Switch the Version control to visible Meta Files
3. Create a folder in the project
4. Open your finder
5. Navigate to the folder
6. Delete the folder (leaving the meta file intact)
7. Return to Unity
Expected result: The folder is deleted
Actual result: The folder is recreated upon opening Unity

This only happens when using the visible meta files version control. If the default (hidden meta files) is used, the folder does not get recreated.