I believe the solution will be to find and change the site set-up for the site that Dreamweaver thinks is already using the folder your folder is inside of. By that I mean you’ve probably already set up a site and entered the root folder in Dreamweaver. This could be any folder, including your main documents folder — all Dreamweaver knows is that the folder is already set up for a site and now you’re trying to set up another site within that folder in a way that could lead to problems when you upload your new site.
The solution is to edit the site information for the site that contains the "same" folder and either delete the site definition in Dreamweaver or change it to another folder. Even if you’ve deleted the actual folder, if Dreamweaver still thinks it’s in use, you’ll run into this conflict.
Check all sites definitions...