Upon cutting the users across, many users complained the data was approximately 7 days old which is the approximate time I did the initial robocopy. After further investigation it appeared DFS-R was not keeping the data in sync and many directories had not been replicated. These files and folders which were not replicated also did not appear in the backlog count under DFS-R Health Reports which were run to verify replication status.
It turned out the cause of this issue was because the "SYSTEM" permissions were missing from many directories in the file server structure. As the DFS-R service runs under the "SYSTEM" account, it must have access to the data in order to perform replication. Robocopy was however able to move this data as it was running in backup mode which uses VSS to snapshot the data.
This directory structure utilised block policy inheritance numerous times throughout the folder structure and as a result finding directories which did not have SYSTEM permissions configured correctly was a challenging task. As a result I wrote a PowerShell script which performs an audit against a directory structure and returns all folders which are missing the "SYSTEM" permission so that an Administrator can manually add the missing permission at all folder levels with inheritance broken.
This is a handy script and I posted it online for everyone as I recommend running it against any directory structure on file servers to ensure the SYSTEM account has full control over all data, a recommended Microsoft best practice.
I hope this PowerShell script helps other people out there!