Assuming you are talking about a normal IMAP e-mail . The the way to clean out the trash is to go to your fav computing device (not your Droid) and fire up the e-mail client and empty the trash.
When the droid connects again, life will be good
I have the droid, a mac (using OSX email client), and a winbox (using The Bat email client) all getting the same emails from the same pop3 server.
short of deleting them on the server, I can't see how anything done on the desktops can affect the droid's collation of deleted emails. In fact, it does not.