If the folder where you put your backup copies of your icons is on the desktop, you may find that when icons disappear from the desktop they'll also disappear from the folder on the desktop.

Your icons backup folder may need to be "anywhere but on the desktop."

You probably can safely put a shortcut to the folder on the desktop, but I'd recommend that the folder full of shortcuts should be somewhere else, at least until you figure out why some are disappearing.

When icons are removed from the desktop, the program files that their shortcuts point to are not removed, I presume, so a folder that a desktop shortcut points to/opens should have its contents undisturbed.

Microsoft BDSM appears to be telling you that the shortcuts/icons it removes are defective in some way. Perhaps some investigation into whether the programs that they open are "Win7 compatible" would be productive?

The Win7 manager checks for errors when the system starts, but "web gossip" indicates that it can also detect errors while running, and may reboot itself unexpectedly if it finds something significant. It apparently can only make (some) repairs during a boot cycle, but a repair boot may not log you in by your normal "username," especially if it needs a "Safe Mode" to make the repairs. The disappearance of "all of the icons" may just be because it's booted to a "dummy username" that has no icons on its desktop. A reboot with your own username/logon may show a completely different desktop, since each user must set up a "user specific" desktop.

The most widely reported annoyance I've seen with the SM repairs is that it generally can only fix one error (or few) at each reboot, so if there are several significant errors it may go into what appears to be an "infinite cycle of reboots." (A virus/trojan that reinstalls itself each time Windows opens could create a true never-ending-cycle.) Eventually it should get everything fixed in most cases(although some people say the reboot cycles never end). When it finally settles down it may open as user "Guest" or "Everybody" or as "Administrator" with a desktop that you've never added any icons to.

If this might be what's happening you might find that changing users to make sure that you're logged on with your normal logon name (reboot and logon normally or "change users") may show a different set of icons. (?)

But I'm only guessing.

John