Not sure what "trashed" means. When I did it (if I recall correctly), Windows desktop disappeared and VM was using Mac desktop. That is the only way it can work, as when you switch off the VM, Mac desktop still exists while VMs desktop is not there. So mac cannot use VMs desktop...
Therefore, if you share desktop, it really means that Windows will use Mac desktop. You can add icons to Mac desktop of Windows stuff, but when you switch VM off, those become kind of orphans. I think Parallels has some 'clever" solution - I think the VM gets started when you click on something belonging to VM stuff...
As I said before, sharing desktop becomes confusing, but if you think about the logic (Mac exists always, VM stuff only when VM is started...), it is quite logical and reasonable solution.
Oh yes, and if you ever find really robust solution for not loosing desktop layouts - in Windows OR Mac - let everyone know. I tried every I could find.
I stopped counting how many times my carefully designed desktop was reset by OS (Win or OSX) few years ago :-(