NTFS permissions are stored as part of the file system itself, in an attribute in the Master File Table. So the backup and restore of NTFS permissions is somewhat different than Share Permissions. Windows Server 2008 r2 is comes with a native utility to fulfill this purpose.
I used the following command to backup and restore the NTFS permissions:
Backup and Restore NTFS:
icacls E:\Users\* /save C:\NTFSPerm /T /C
The /T switch recourses through the directory to get sub folder and files, while the /C switch continues on error.
Restore:
icacls E:\ /restore C:\NTFSPerms.txt /C
When restoring the NTFS permissions only include the drive path and use the /C switch to continue on error.
ICACLS Wiki
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