I would first start with making sure you only have one design of each template om the servers.
Make sure acls are set that changes only propagate down to the mail servers
Sign each template with a admin id from you company,
The nconvert command is best for insuring that all design elements are including folders are set on the mail folders to be based on the template name correctly. I would suggest having this run as a program doc scheduled for weekly (weekend is the best )
Design task really no longer needs to run daily and should be controlled via a program doc