You cannot recover data from projects after you have permanently deleted them. If you accidentally permanently deleted a project, use Contact Us and explain what you deleted, as the Scratch Team can still recover it.
To delete a project from the website, go to your My Stuff page (make sure that you're logged in). Scroll down until you see the projects that you want to delete. If your project is shared, click "unshare" next to the project, then click "delete." If your project is already unshared, you just have to click "delete." To permanently delete it, go to your trash and click the Empty Trash button, then confirm your password. The project is now permanently deleted. To delete projects from your hard drive, delete the .sb, .sb2 or .sb3 file like any other.