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Not using Drupal at the moment but may come back to it some time.

To update sites by ssh use

cd /home/USER/public_html/sites/SITE-FOLDER/ && drush vset update_check_disabled 1 -y && ls -l && drush cc all && drush rf && drush up -y

Repeat for each domain by adding

&& cd /home/USER/public_html/sites/SITE-FOLDER/ && drush vset update_check_disabled 1 -y && ls -l && drush cc all && drush rf && drush up -y

Change FollowSymlinks – TO – SymLinksIfOwnerMatch on some servers to make it work