Windows 2012 File System Deduplication

Problem:
Doing a normal backup of a file system with 2012 Deduplication turned on, may cause files to restore with 0 data
Solution:
In the file set editor, put a check in the "Ignore Win32 Attributes" and add an exclusion to ignore the System Volume Information. This will allow for Backups and Restores to work normally.

Because the backup is not Windows Deduplication aware, it will backup the un-deduplicated amount of data stored on the drive. This is not a problem since the files will be re-deduplicated once they are on the RAID.
You might see a negative side effect if you are attempting to restore the same directory the backup came from, and may not have enough free space to restore the un-deduplicated data. To get around this you may have to run smaller restores and manually run the deduplication optimize command from power shell to force the deduplication of files.