The method I used was to firstly access the HostRoot folder and make a copy of a file(any file will do) in the same folder. I did the same for the PortalRoot folder. It does not help doing this with the DNN File manager, you must access using a direct method such as FTP. Once you have done this you can then do a recursive sync in the file manager. I found then that the folders were all available and the files were visible. It looks as if a change must take place in the folder structure first for the system to recognise that a change has taken place and then to syncronise correctly( a wild guess but I have been able to replicate and verify this)