The issue occurs when you have a volume that is configured for deduplication in Windows and it is also replicated using DFS Replication (DFSR). If you create a backup job and select DFSR in the backup selections, the volume’s chunk store is backed up.
Note: The chunk store is only backed up when DFSR is configured to replicate the entire volume and not just a share on the volume.
For example, you have a volume E:\ on a Windows Server 2012 computer which is configured for deduplication. The entire volume is also being replicated to another computer by DFSR. When you back up this computer and select DFSR in the backup selections, the chunk store on E:\ gets backed up.
Deselect the deduplicated volume’s System volume information\Dedup folder under DFSRReplicatedFolders in the job’s backup selections.
Note: when you back up the deduplicated volume directly instead of backing it up using the replicated instance, Backup Exec skips the chunk store automatically.