Unintentional side-effect of the new .gitlab_workhorse_secret

Since gitlab 8.12 has been released my daily backup script fails as soon as the omnibus package update is applied on my system via up2date.

I’m getting the error:

rake aborted!
Errno::EACCES: Permission denied @ rb_sysopen - /opt/gitlab/embedded/service/gitlab-rails/.gitlab_workhorse_secret

And I need to do a gitlab-ctl reconfigure in order to get my backups working again. Is there a way to get the upgrades & rake backups working again without manual intervention?