Change Permissions in Bulk

I am using backup software which runs as a service using the administrator account. It's supposed to be backing up users shares but the a bunch of files keep getting skipped. The reason is because the administrator does not have security permissions to those shares. I would then go ahead and grant the administrator full security permissions for those user shares. I would also run into another problem. Some user shares are owned by the user and when trying to open the share is says access is denied. I would make the administrator the owner but then I would have to re-grant that user permissions to his/her own share because by doing that it gets rid of all permissions for that user. This wouldn't be a problem if it only happened to one user. However this is happening to 100's of users. To change these permissions individually would take a really long time.

Is there any way that I can make the administrator the owner to all of those users shares (in bulk) without having to re-grant user permissions to the folders.
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You can change ownership without affecting permissions using Subinacl.

subinacl /subdirectories "d:\root folder\*.*" /setowner=domain\username

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eshiramAuthor Commented:
How exactly do I use it I tried running subinacl but no command prompt came up.
eshiramAuthor Commented:
The CMD screen actually does come  up but then disappears.
Subinacl is purely a command-line tool.

Open a command prompt first by going to Start|Run, entering cmd, and hitting OK.  Either place subinacl.exe in the Windows directory, cd /d to the directory where it's located, or preface your subinacl commands with the executable's full path.
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