restore issues with Virtualmin

We had a server melt down. So we built a new Ubuntu 8.04 server with postfix and the other pieces. Then restored the backup. The big problem we have now is that most mail boxes have two mail dir's. i.e mail Maildir
The old server was a Ubuntu 6.06. Is there a way to rescue old mail or tidy it up so the users have just the one set of folders like inbox sent drafts and not a second set of these?