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This happened on both a linux machine and an os x machine.
1. On linux - I downloaded .torrent files and used them to download movie files. All the files were downloaded into ~/tmp/torrents. I moved ~/tmp/torrents into /tmp/torrents, then I moved /tmp/torrents back to ~/tmp/torrents. When I restarted my machine, the directory ~/tmp/torrents and the directory /tmp/torrents were no longer on my file system. I did a sudo updatedb and a locate, I could not find my files.
2. On mac - I downloaded .torrent files and used them to download movie files. All the files were downloaded into /Users/me/torrents. I moved /Users/me/torrents into /tmp/torrents, then I moved /tmp/torrents back to /Users/me/torrents. When I opened up the directory /Users/me/torrents, a lot of the movie files had disappeared, mainly movie files that were in /Users/me/torrents/A.DiVX.movie/* - so all directories inside of /Users/me/torrents were empty - except, I noticed directories inside of /Users/me/torrents/*/* that I had already played. Again I did an updatedb and locate, but was not able to find my missing movies.
I can't say anything about the folder in Users/me or ~/tmp (by which I presume you mean /home/<your username>/tmp") , but it is common for Linux systems to be set to clear the /tmp folder at boot time. "tmp" stands for temporary - it is a common location in which files are saved temporarily when they are downloaded. but in order to be kept permanently they need to be saved to another location.