NTFS permission removed when deleting a subfolder

Hello everyone,

I do have a very strange issue with my file server. Let me first describe the infrastructure.

OS: Windows Server 2016
Roles: File and Storage Services
Type: Member of a 2016 Domain

On the file server I do have to following structure/permission:

• F:\
  • ANWDTest
    • ZZZ
      • DIMS
      • Wagenbuch

The NTFS permissions to those folders is like that:

• ANWDTest
  Inheritance disabled
  CREATOR OWNER - Full control - Subfolders and files only
  SYSTEM - Full control - This folder, subfolders and files
  Administrators - Full control - This folder, subfolders and files
  L_NTFS_J_R - Read & execute - This folder only
  
  
• ZZZ
  Inheritance enabled
  L_NTFS_J_ZZZ_R - Read & execute - This folder only
  
  
• DIMS
  Inheritance enabled
  L_NTFS_J_ZZZ_DIMS_R - Read & execute - This folder, subfolders and files
  L_NTFS_J_ZZZ_DIMS_W - Modify - This folder, subfolders and files
  
  
• Wagenbuch
  Inheritance enabled
  L_NTFS_J_ZZZ_Wagenbuch_R - Read & execute - This folder, subfolders and files
  L_NTFS_J_ZZZ_Wagenbuch_W - Modify - This folder, subfolders and files

So far I think this is nothing special, now here is my issue:

When I delete the "Wagenbuch" or the "DIMS" folder this does remove the group "L_NTFS_J_ZZZ_R" from the "ZZZ" folder AND does remove the group "L_NTFS_J_R" from the "ANWDTest" folder... and I do have absolutly no idea why this is happening.

Does anyone see an error in the setup or did face similar issues? I am totally lost here, even no idea where to start searching.. Google did also not help at all.

Thanks for the support!

UPDATE 1: To be sure that is not an issue of our file server - I did setup the same structure on an other 2016 server, and did face the same issue.

UPDATE 2: In the meantime I did the same setup on a 2012 R2 server and there is no issue at all, so this seems to be related to Server 2016.