When you look at the file manager in DNN that is under either Admin > File Manager or Host > File Manager, it does not show all of the files on your website.  It only shows the files that are under the /portals/_default or /portals/# folders.

This is by design.  The DotNetNuke file manager only lets you manage files in those locations.

If you would like to manage files that are not under the /portals/ folder, then you will have to use FTP to do that.

Your DotNetNuke site is not showing all of the files in the /Portals/ folder, then you may need to synchronize the files system.

1)  In order to do that, select the root folder, and click Snychronize.
2)  You may have to repeat this process a couple times.
3)  You may need to refresh the page that has the file manager module on it.