There is an article where they explain a possible Data loss when recovering individual files from a backed up Windows Server 2012 deduplication volume. (link to the article below)

https://support.emc.com/kb/453689

According to the article is safe to backup Windows Deduplicated volumes if you use the following string

VSS:NSR_DEDUP_NON_OPTIMIZED=yes

** For Networker 8.x

Within NMC navigate to:

Confiiguration> Clients > right click on clients>properties> Apps & Modules>Save operations box

Add the string

VSS:NSR_DEDUP_NON_OPTIMIZED=yes

All Windows Server 2012 deduplication volumes will be backed up unoptimized, and will be recoverable, when this flag is set

**Also be aware of the changes in your backup after turning off the optimization, as you may face increases in the amount of data backed up.