(Just to clarify: things went into a folder, not a file
)
Well, while mys suggestion would be to make the files go to the Shared folder instead of the Root, if you want to move the previous 50 dlds into the new folder open a browser window and browse to the Shared folder, then open another one, browse to the Root folder and drag-and-drop the files from one folder to another.
After that, open Limewire, go to the Library and click refresh, then go to Tools, Options and Saving and make sure that the saving directory specified there is the Root folder and not the Shared folder, otherwise new downloads will just go to the Shared folder again.
Don't forget to click Apply after yur' done.