I find on certain server setups, the imap folders on my server don't connect with that specific web application. I would say that you can drag each of those messages into the corresponding folder on your web application (the proper sent folder, etc), and delete those folders accordingly in your personal settings > folders. However, I'd check with your hosting company about that first -- while I've never had a problem on Debian or OS X servers, their setup could be much different.

--
Brady J. Frey
creative director // dotfive