In DNN 3.3.0 / 4.3.0 new file storage types had been added: SecureFileSystem and SecureDatabase, that prevent external access by simply entering the URL (like www.mydomain/portals/0/myfile.gif). To implement this, the controlling information is stored now in the Files and Folders table of the DNN database and no longer retrieved from file system. If files have been added manually using FTP or windows file manager, the Files and Folders tables need to be updated - or synchronized. This will add all missing entries and, since ~ 3.3.7/4.3.7, even delete orphaned entries. A recursive sync will not only check files in current folder, but as well in all subfolders. For many situations, it is convenient to use "auto sync" in Host Settings, this will synchronize a folder on access - but might not make subfolders to show up or remove orphaned folders, therefore please use the command in the file manager, if you are missing files or folders or want to remove orphaned entries. The synchronization subject is not trivial and has been improved multiple times, therefore migrating to the current DNN version will lead to best results.

If Sychonize Database fails, it is most likely, that you have files with apostrophes ( ' )  in its name, duplicate entries in file or folder table, that might need to be removed manually.

HTH