Hello Rolf,
Thanks for the inquiry. You may want to review our Knowledge Base article on restoring a user mailbox.
Although this is similar to what you are trying to accomplish you may want to consider taking the same steps except either removing the content of the mailbox folders and remove the mailbox.cfg files in each folder. I presume that you are looking to use the same folders but not carry over the emails ?
Please let us know if you have any questions and open a Support Ticket if you need further assistance.
Thank You.