Backing up the file system in Windows 2012 with deduplication turned on may cause files to restore with 0 bytes of data.
Steps to resolve
In the file set editor, select Ignore Win32 Attributes, and add an exclusion to ignore the System Volume Information.
Because the backup is not aware of the Windows Deduplication feature, it will back up the undeduplicated amount of data stored on the disk. This is not a problem since the files will be deduplicated again once they are on the RAID.
You might see a negative side effect if you try to restore the same directory the backup came from, and may not have enough free space to restore the undeduplicated data. To get around this, you may have to run smaller restores, and manually run the deduplication optimize command from PowerShell to force the deduplication of the files.