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Every single time I hook my Droid 3 up to my PC to transfer files to or from my phone, most (but not all) of my icons on my home screens disappear. It doesn't matter which mode I set it to, PC Mode, Mass Storage, etc. Reboots don't help.
If you don't want them to disappear...yes. They need to be available to the system at boot, essentially the launcher needs to see them at boot. When moved to sdcard (media) and you mount the storage to your PC, you are dismounting the sdcard from the system, cutting the connection the phone has with those apps stored there. Remounting does not restore that "system" connection. A reboot will/should restore it. Also if you can force the launcher to restart that will fix it...though give it a few seconds to scan the sdcard and add the found apps to your system. LauncherPro has a Restart Launcher option that makes it simple to do this.
Otherwise, don't mount the storage to the PC, use Dropbox or FTP or even ADB (USB connected ad Charge Only).