What, *specifically* does Windows 8's “Refresh Your PC” option delete and retain?
Microsoft explained it in detail here:
Refresh functionality is fundamentally still a reinstall of Windows, just like resetting your PC as described above, but your data, settings, and Metro style apps are preserved. We have a solution to help you with your desktop apps, too, which I’ll talk about a little later.
So you must reinstall all your desktop applications.