I had the same problem of everything on my desktop disappearing after installing Monterey in November. The desktop was backed up to iCloud, but the files weren't there. I went through a whole thing with AppleCare, hours and hours of it, looking for the problem. I even restored everything from a pre-Monterey backup. The desktop repopulated but then I, and the support person, watched in real time as those files deleted themselves one by one! They weren't findable anywhere, not trash, not hidden. I was bumped up the food chain to higher level tech support. Still no explanation. I had other things to do so I let the problem sit for a month while new updates of Monterey came into being. When I finally went back to talk to AppleCare, they determined the problem was with Dropbox symlinks, but it wasn't, I found out Dropbox stopped using symlinks over a year ago. So I was back to calling AppleCare again.
Long story short: I decided not to bother talking to Apple again, since Monterey in its new update is no longer (apparently) deleting desktop files. And the last time I spent hours with AppleCare the person seemed to have no idea about the problem (and even claimed that she hadn't heard of any problems with Monterey and data loss, huh?). I put all my desktop files back where they were before, on my desktop, from an external hard drive backup from October, and they seem to be staying put. I just hope there isn't any other data loss that I'm not seeing.
Does anyone know if there's a problem with using the desktop as a filing system? Is it inherently unstable? I'm kind of attention deficit, so having everything out there and visible works for me, but it seems to me it has the potential to cause trouble.
I keep hearing all these different problems with Monterey, time consuming disasters, from many of my friends, is Apple explaining any of it, or taking responsibility?