AFAIK, since Buffalo does not give out Root access (/sadface), you must delete the ROOT level folder (IE the main folder under shared folders where you selected for the backup job), its not fun, and I have read of horror story's about days of copying files to a NEW ROOT level folder in order to get rid of them...
From what I read cringed about, it seems the Backup and Replication process (TeraStation only), uses the root user or a root level account to PREcreate both the files/folders (padding?) and locks them for its exclusive use, then starts the procedure! The issue it seems here is that if the Backup/Replication error's out, or is interrupted by anything other then what is considered NORMAL operation (completion?), while the process stops, the lock by the root/root level user is not removed... thus making deleting/removing files/folders that did not copy successfully an operation you "dont have access" to do...
Along with my other big want (an empty folder/s trashbox option in the WebGUI), I wish they would put a "ReAlign Permissions" button on the shared folders page, so if something like this occurs, you could simply use the button to remove the root permissions (since, ya know, you AREN'T root) and restore whatever access restrictions you have setup on the shared folder! Of course there would have to be other checks to make sure a backup/replication procedure isnt running, but this would solve this issue outright! (not to mention strip pesky NTFS permissions that sometimes manage to "inflitrate" when you copy it to the LINUX XFS/EXT3 partitions!)
Hope this helps your issue.