What is the OS on the device? There used to be an issue on4.2.0.73 OS devices where Desktop Manager would remove things from the device. However, you have to have run application loader in order for it to do that. If you just did a backup/restore it shouldn't have removed anything.
Go to Options >Advanced Options >Host Routing Table >hit Menu key and select Register Now.
Also, did you have the device plugged in while attempting to view the contents of the media card? You can't see the card while the device is plugged in. Unplug it and you should see it.
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