When you start WED it seems to default to the last folder were a project was saved. If that project folder no longer exists, then WED recreates it. This should not happen, in my opinion. After I complete a project, I remove the folder to a backup hard drive to free space on my work hard drive. The next time I open WED it recreates the folder structure from the removed project.
For example, if I create I was saving WED files to the following place:
D:\work\project name\game files\WED file\
And then I remove the entire "project name" folder to a new drive, then the next time I start WED it recreates this entire folder structure!
Please change WED so that it does not do this. WED should not create ANYTHING unless the end-user tells it to.