DFSR Backlog Stuck on Non-Existent Folders

This is a slightly stale question but have you explored the 'Staging' and 'Conflict and Deleted' folders?

DFS Staging and Conflict and Deleted Folders

One way that you could end up with this situation is the presence of leftover files or fragments floating around in these folders that are not getting properly resolved. You could clean out those locations to manually 'reset' synchronization on both sides. However, I'd also investigate the source of the folder and ensure that:

  1. Conflicting permissions are not being set on the files/folders in question.
  2. Another server or endpoint is not repeatedly creating this folder because of an old or misconfigured script or synchronization task.