When I go to link to some files I uploaded to the root Assets folder through my ftp client, they don't appear in the the drop down menu when I go to link to them in the CMS admin. Also, files that I've deleted in the root Assets folder are also still appearing.
I would not recommend you manipulating the assets folder with a FTP client. SS does a lot of checking and data collection around assets that are uploaded through the CMS. This includes the creation of corresponding database entries.
Is there some reason you would not be using the provided upload facility in the CMS Files and Assets tab?