Hi Dave,
There is nothing in X-Plane or WED that would prevent you from moving the custom scenery file. You should be able to drag and drop the folder, or copy and paste it wherever you want it. If you are not able to do so, it would have to be an issue with the permissions setting on your computer.
If you move the file and still need to work on it in WED, you can simply point WED to the other X-Plane install on the initial screen (use the "choose X-Plane folder" button).