It sometimes looks like you have not successfully saved a project from Scratch Desktop because when you try to open it the editor, it appears blank. This is a known bug, but it's not with saving, it's with opening a project with Scratch Desktop. Double clicking on a Scratch Project from your operating system (or opening in a similar way) won't open it in Scratch Desktop as you might expect.  

However, if you open Scratch Desktop first and then choose "File" > "Load from your computer" and choose your Scratch project, it should open just fine.