If a file happens to be located in the same directory on both the primary and secondary storage, the file name is listed twice in the directory listing. However, all file operations are directed to the file on the primary system.
To resolve this problem, you can rename one instance of the file to make both versions of the file available under different names. Then open the files to determine which version to keep.
You can control how DST handles duplicate files by configuring global policies. For information, see Section 8.3, Resolving Instances of Duplicate Files.