[Dovecot] Missing folders

I've recently had a oops with the system I was running dovecot on so have had to move it to a new machine, I've been able to retrieve the mbox files from the old machine, built the new machine and over wrote the new mbox files with the old one in maildir, connecting to the server via imap woeks but I can only see the mail in the inbox from the old mbox files, emails in sub directories (the sub directories arn't there), is there some command I need to run to get it to pass the mbox file to find the folders or it there another file I need to transfer form the old machine.

(I'm assuming that all the emails for a user, including those in subfolders are within the single mbox file, particularly as I'm is very large)

Thanks

John