Remotely setting permissions on the folder at the root of the share removes all inherited permissions from the root folder and all subfolders. To set permissions without removing the inherited permissions, click No and either change the permissions on a child folder or make the change while logged in locally. Do you want to continue?If the user chooses to apply, the original ACL is cleaned up, and only leaves the newly added ACE in the ACL.
If the user wants to add explicit permission for certain users on the root folder of the share, it is recommended to do that by modifying the Share Permission from Windows Computer Management (compmgmt.msc).
For example:
If the user wants to only allow user A to access the shared folder, they can remove everyone from the Share Permissions tab of the share in Computer Management and add user A with the wanted permission explicitly.
Some users are exporting the subfolder of the root folder of the file system in order to hide the /.etc and lost folder in front of end users. In that case, the user can modify the permission on the root folder of the share using either of two methods.
For example:
The user exports the subfolder sub1 of the file system fs1 with local path /fs1/sub1. If they want to change the NTFS permission on the sub1, they can export the root of the file system /fs1 as a share, go to this share, and change the permission on sub1.
For more details on how share permissions and NTFS permissions work, see Microsoft article below:
https://docs.microsoft.com/en-us/previous-versions/windows/it-pro/windows-server-2003/cc783530(v=ws.10)?redirectedfrom=MSDN