Use the following PowerShell script to backup NTFS permissions.
Permissions Only one folder (no subfolders):
Get-Childitem -path \\server\path\folder | Where-Object {$_.PSIsContainer} | Get-ACL | Select-Object Path -ExpandProperty Access | Export-CSV c:\tmp\ntfs.csv
Permissions With subfolders (-recurse):
Get-Childitem -path \\server\path\folder -recurse | Where-Object {$_.PSIsContainer} | Get-ACL| Select-Object Path -ExpandProperty Access | Export-CSV c:\tmp\ntfs_subfolders.csv