Upgrade source to omnibus - migrate secrets

in the source installation (currently 8.0.3 in my case) there is a secret file at /home/git/gitlab/.secret. It contains only one hash. At the omnibus install there is the file /etc/gitlab/gitlab-secrets.json which contains secrets for gitlab_shell, gitlab_rails, gitlab_ci and mattermost. How do I migrate this .secret file?

I wasn't able to find infos in the documentation at http://doc.gitlab.com/omnibus/update/README.html#upgrading-from-a-non-omnibus-installation-to-an-omnibus-installation or https://gitlab.com/gitlab-org/gitlab-ce/blob/master/doc/raketasks/backup_restore.md

If I don't migrate the secrets I 'only' loose the 2 factor authentication. Or do I loose something else?