Gitlab upgrade failing and gitlab-ctl reconfugre failing

As of an ongoing maintenace the system upgrade is being done.
we currently on v11.7.5 and need to move to version 12.
In line with the guidelines we are moving from 11.7.5 > 11.11.8 > db upgrade > 12.0.x > !2.newest.
However the first step moving to 11.11.8 fails
Malformed configuration JSON file found at /opt/gitlab/embedded/nodes/localhost.json.
This usually happens when your last run of gitlab-ctl reconfigure didn’t complete successfully.
This file is used to check if any of the unsupported configurations are enabled,
and hence require a working reconfigure before upgrading.
Please run sudo gitlab-ctl reconfigure to fix it and try again.
and gitlab-ctl reconfigure fails with
here was an error running gitlab-ctl reconfigure:

storage_directory[/registry/backups] (gitlab::gitlab-rails line 116) had an error: Mixlib::ShellOut::ShellCommandFailed: ruby_block[directory resource: /registry/backups] (/opt/gitlab/embedded/cookbooks/cache/cookbooks/package/resources/storage_directory.rb line 33) had an error: Mixlib::ShellOut::ShellCommandFailed: Expected process to exit with [0], but received ‘1’
---- Begin output of stat --printf=’%U’ (readlink -f /registry/backups) ---- STDOUT: STDERR: stat: missing operand Try 'stat --help' for more information. ---- End output of stat --printf='%U' (readlink -f /registry/backups) ----
Ran stat --printf=’%U’ $(readlink -f /registry/backups) returned 1

The system being is clone of out production created to test the upgrade process.
I have manually created new backups off the test system which succeeded but I am wondering why reconfigure is moaning about the backups. The system otherwise healthy.