Is there a reason why you're not using a "real" FTP program?
DW has been known to damage things badly, especially when doing mass uploads/downloads.
Plus, renaming files/folders in DW can be risky especially if you allow it to "automatically" refactor any of your changes into any of your files.

Besides, a proper FTP program will let you "move" the files and folders to another directory without having to download+upload everything.