This is really intended behaviour: If a shortcut doesn't exist, don't show it.
Try loading the last snapshot after you mount the drive. That should restore the shortcuts.
Drive mounted, shortcuts created and fenced. Snapshot taken, drive dismounted, right-click desktop and Refresh - shortcuts disappear from fence. Re-mounted drive, restored snapshot, shortcuts remain gone even after right-clicking and choosing Refresh on desktop. Edit: they appear to have moved to my "Unsorted" fence, where I put all new icons by default on the desktop.
I would revisit why you chose to hide/move shortcuts that point to a volume not accessible or visible. That includes encrypted volumes, hot-swap drives like USB sticks, etc. Requiring someone restore a snapshot to restore hidden shortcuts is too tedious, in my opinion. They may have made/changed other fences since the last automated daily, and this would cause no end of trouble when it reverted.
As a fences user, I would simply like to see shortcuts remain where they are, and utilize default Windows behavior for shortcuts. If their drive isn't accessible, they simply timeout. If you'd like custom behavior, you could dim their icon or make it slightly transparent to indicate the file they point to isn't available.