Currently the only way I can do this is to open the .torrent file in Azureus and use that to change it. And that I can only do before I import it into Transmission.
Often I have the problem that the tracker a torrent's using in Transmission dies for a few days, and the only peers I can connect to are from PEX which is really annoying.
There is a big controversy over this right now, too long for me to explain it all here, but read that post and it becomes clear. Some users may just blame the torrent client for slow downloads without knowing.
You can get around it by simply deleting the moviex tracker from torrents and keeping the public tracker, but you can't do this in Transmission (yet).
It shouldn't pose any problem with already-running downloads because the metainfo dictionary (where "announce" and "announce-list" are located) isn't used to calculate the final file checksum (though my understanding gets sketchy).[/url]