I assume that it is Maildir as that is the name of the folder located in the user folder. I also know that the server is setup for imap so it should provide me with that option as well.
So, if I backup the mail (user folders), reinstall the server and install ISPConfig I can simply restore the backups to the newly created maildir folders of ISPConfig?
Now that sounds like a solution I can live with. Thanks for your quick reply.