fix: soft delete empty repository records (batch 3)

mentioned in commit edb90203

mentioned in issue #597 (closed)

mentioned in merge request gitlab-org/build/CNG!899 (merged)

mentioned in merge request gitlab-com/gl-infra/k8s-workloads/gitlab-com!1536 (merged)

mentioned in merge request gitlab-com/gl-infra/k8s-workloads/gitlab-com!1537 (merged)

mentioned in merge request gitlab-org/charts/gitlab!2397 (merged)

mentioned in merge request omnibus-gitlab!5925 (merged)