Stolen Macbook found with Prey, only files, NOT folders, are missing

Prey worked perfectly to get the cops to go to the thief's house!
My Macbook Air OS X Lion is safe now. All the programs I installed are still there, and my folders are still exactly in the same positions. Even the subfolder in a folder I named my ebooks is still in the same position at the bottom of the finder window. The folders are untouched but anything that is a file is gone. It doesnt seem to be a reformat because my programs that are meant to run (BOINC) in the background still start up and the folders would be gone.
How is this possible? Is it possibly a feature of Prey or Macbook security that I have misread? I cannot find it.
Even my Dropbox was made empty and my wallpaper was blank because the image file was gone. Desktop empty too but my organization structure for the comics and icons I collect are in tact.

Thanks. Thats what I thought too but I found it so strange that dozens of my folders were empty, even folders inside folders were still there, but no folder has been deleted. It would take a really long time to only delete files inside folders, but not my folders. Like I divided my internet collections stuff into postsecrets and deviantarts, which had smaller folders by category. These were all empty but still there. How could he have deleted like this?

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