You can run this script as a cron/scheduled job on your host to replace the cms-data folder contents with a templated version that you may have. You will need to replace the paths to the cms-data folders inside this script in order for it to work.

replace-cms-data.sh

#!/bin/bash
rm -r /home/username/websites/total-cms.com/cms-data/
cp -r /home/username/websites/total-cms.com/cms-data-template/ /home/username/websites/total-cms.com/cms-data/