If I try to rearrange the shortcuts to app icons on my homescreen, sometimes they disappear. It happens to all apps, bookmarks, and folders, too: even stock apps, like Play Store. I have an LG optimus s that I got about a year ago, new. I'm running 2.3.3. Gingerbread. Details : app icons often reappear in folders after reboot, sometimes without reboot. I'll say again, for clarity, that this only happens when I attempt to rearrange the icons : no spontaneous disappearances! I use my phone almost 24/7, as I do not own a tablet or a computer with wifi, so I like everything to be in it's place.
are you using the stock launcher? Clearing all data from your launcher app should sort of reset your app. You can try that from Settings -> Applications -> (Launcher App) and then hit the "Clear Data" button. You will lose your homescreen settings preferences.