Downloading Large Folders From Dropbox

There doesn't seem to be a way to do this at the time. Using Windows shortcuts is one possibility to make it as though the files are located in the same folders, however, it seems like it would get a bit complicated if there are a lot of folders.

There is a feature request for this exact issue, which you can vote on.

Other features you may want to look for is the ability to watch any folder, which you might be able to use in conjunction with your file system to create a limited set of folders to sync. Another one that might help is excluding certain file extensions, this would help if all the large files are of the same type (e.g. .exe, .avi, etc.).

I am not sure whether this will answer you. While you create a folder in your system, it will be sync with the web account, which may take few seconds of time. If you rename or move the folder, whose sync is in process, the sync will be completed with new folder in web and then the second request to rename will be in process, but at the same time, as you have renamed or moved the new folder, the web will sync the desktop version which results in duplication. When this happens to me often, my practice is to wait for the sync to complete before starting the second task related to the same folder.