I have managed to get the original folders to syncronise after upgrading from 4.0.3 to 4.3.5.( I wish I had never done it!!).

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)

I found that this does not work for Firefox. The security settings are not even visible in Firefox! I did try to delete a file from the file manager while I was in Firefox. I got a message stating that the filemanager did not have access to the file. When I checked the file had been deleted anyway!

I hope that this might be of some use to someone!

This looks to be an enormous issue for which no-one wants to take responsibilty to fix!! No-one from the Core Team appears to see this as an issue!! Does anyone really care!

DuncanF 

This is a bug - I'm experiencing it too on any version of DNN with the new file/folder structure.

The file manager is virtually useless as well as any of the file-picker controls in any module for this reason.

I'm also somewhat saddened this hasn't been acknowledged and addressed by the core. I've been with DNN since version 1.xx and this is one of the worst bugs to date.

As always, I'm thankful for the framework and the core, but guys, please take a look at this. The file sync routines do not work correctly in the file manager - even on clean installs.