*ouch*
I'm sorry you've had so much trouble!

I checked the Fetch site to see if this was a common problem, and all I could find was that Fetch does allow mirroring, which would do exactly as you describe. Is it possible you have a configuration option set to always mirror?

The alternative would be navigating through the file structure and uploading each individual file, or seeing if you can merge the files on your computer first (but then you would be uploading the entire site again, which would not be great).

You might want to wait for the update (tonight or tomorrow at worst...I'm finishing up the last of it now) and try then if you do have to upload it file by file (so you won't repeat yourself).

-Ng_