Q:

Cronjob started rollback and files were deleted. Why?

I faced a strange behaviour. First, I setup cron jobs as described in http://devdocs.magento.com/guides/v2.1/config-guide/cli/config-cli-subcommands-cron.html. Then I changed file permissions to dev mode (writeable). When cron jobs have started, files were being deleted. As soon as I noticed this, I changed file permissions back to recommended for production mode and files stopped disappering.
Cron Daemon email (Subject: Cron  /usr/bin/php /home/[my-domain]/public_html/update/cron.php):

..........
PHP Warning: 
  unlink(/home/[my-domain]/public_html/[my-domain]/.git/hooks/post-update.sample):
  Permission denied in
  /home/[my-domain]/public_html/update/app/code/Magento/Update/Rollback.php
  on line 157
PHP Warning: 
  rmdir(/home/[my-domain]/public_html/[my-domain]/.git/hooks):
  Permission denied in
  /home/[my-domain]/public_html/update/app/code/Magento/Update/Rollback.php
  on line 155
...........

/var/log/update.log:

[2017-03-23 17:00:03] update-cron.INFO: Job "rollback
  {"backup_file_name":"/home/[my-domain]/public_html/var/backups/1480414203_filesystem_code.tgz"}"
  has been started [] [] 
[2017-03-23 17:00:03] update-cron.INFO:
  Restoring archive from
  "/home/[my-domain]/public_html/var/backups/1480414203_filesystem_code.tgz"
  ... [] [] 
[2017-03-23 17:00:49] update-cron.INFO: An error occurred
  while executing job "rollback
  {"backup_file_name":"/home/[my-domain]/public_html/var/backups/1480414203_filesystem_code.tgz"}":
  Extraction from phar
  "/home/[my-domain]/public_html/var/backups/1480414203_filesystem_code.tar"
  failed: Cannot extract
  "app/code/CustomerParadigm/OrderComments/view/frontend/requirejs-config.js",
  could not open for writing
  "/home/[my-domain]/public_html/app/code/CustomerParadigm/OrderComments/view/frontend/requirejs-config.js"
  [] [] 
[2017-03-23 17:00:49] update-cron.INFO: Job "rollback
  {"backup_file_name":"/home/[my-domain]/public_html/var/backups/1480414203_filesystem_media.tgz"}"
  has been started [] [] 
[2017-03-23 17:00:49] update-cron.INFO:
  Restoring archive from
  "/home/[my-domain]/public_html/var/backups/1480414203_filesystem_media.tgz"
  ... [] [] 
[2017-03-23 17:01:00] update-cron.INFO: Job "rollback
  {"backup_file_name":"/home/[my-domain]/public_html/var/backups/1480414203_filesystem_media.tgz"}"
  has successfully completed [] []

Crontab (disabled for now):
# @hourly /usr/bin/php /home/[my-domain]/public_html/update/cron.php%/home/[my-domain]/public_html/var/log/update.cron.log #Magento cron (2)

# @hourly /usr/bin/php /home/[my-domain]/public_html/bin/magento cron:run | grep -v "Ran jobs by schedule"%/home/[my-domain]/public_html/var/log/magento.cron.log #Magento cron (1)

# @hourly /usr/bin/php /home/[my-domain]/public_html/bin/magento setup:cron:run%/home/[my-domain]/public_html/var/log/setup.cron.log #Magento cron (3)

Why have files start being deleted? How to prevent from it in future?

A:

we have this problem with Backup/Rollback procedure, and reported it to magento.
https://github.com/magento/magento2/issues/8017
unfortunately we have lost one magento shop because of this issue, had to restore it from external backup.(good it was under development)
you can leave your comments on that issue on github

