I guess they just use the "reference counting" technique to map multiple "links" to one "physical file",
and I also guest MegaUpload also use the similar mechanism.
This technique works like the "hard link" of UNIX filesystem.

If a MU's link is reported, the link will be dead; however, the physical file will be still alive because their are still some active links pointing to it.
If the server which stores the physical file is down or under maintenance, you'll get a "temporarily unavailable" message.

I don't know how RS removes a reported file, but all links will be dead if RS deletes the physical file.