When you archive, you can select specific folder to archive on, you could leave the inbox unselected and they would not be archived. You could also make it user defined. The user gets to select the emails for archiving.
You will have to copy and paste the mail from the archive back into the production mail file.
You could scratch the archive all together and use just a local replica. which would mimic his production mail file.
What are you trying to achive with this user?