First, this is the installer forum.  If you are planning to use the beta installer, I did have problems when trying to use it with upgrades. It worked fine on new installs.

The upgrade does not have the Desktop module thats true, but that doesnt mean its still not relative.  As a matter of course I recommend making your own backup before installing, especially you web.config, but I have been downloading a complete copy of the site.

Let me warn you , I had difficulties with my site after going from 4.3 to 4.4.1 when I upgraded. Difficulties that I was not able to recover from.  I couldnt add modules to pages.  I wouldnt get any error, the screen would refresh when I clicked on add but no modules would appear in the panes.  I couldnt edit certain modules any longer.

I resync the files , tried reloading, the only thing I couldnt try was deleting and starting again. I needed the hosting company for that and they wouldnt comply for some reason, even when I offered to pay for it.

Bottom line I would contact my hosting company and let them know what I was attempting to do. They may offer to do it for you, which may be the safer route.