We have a problem on all our servers unfortunately with daily updates all Vhost files are turned to default. Also, Everynight apache restarted which is not a good thing for us because we are using wsgi. Anyways until a proper answer or solution comes we just remove the cwp update from the daily cron. If somebody needs you just need to move the file different location.
location is /etc/cron.daily/cwp
mv /etc/cron.daily/cwp /root
will fix the problem temporary.