How to batch download client directorys to win app then batch upload back to web?

I need some suggestions of what is the best way to implement a way for a user that has an online directory and would like to take the files and subDirectorys with them in a disconnected enviroment. I have thought about this for a long time and am now to the point of modeling this part of the appication. And would like to hear some suggestions from someone who has done this before. I know how to get files from a website and to an app and so on.

senerio:
A user has a directory structure and needs to take the web view with them to a windows app in a disconnected enviroment.. User now needs to upload all of these files back to the web app Directory (Overwriting will be fine of old files and directorys if changes have been made) when ready to work online again

Baisically; what is the best implemention of collecting a root directory and all its subDirectroys and download to a client. Then when client ready to work online a roundup is made and root and subdirectroys are uploaded to their webSite

thanks a lot

erik