Add migration to cleanup iid records

db/post_migrate/20190102152410_delete_inconsistent_internal_id_records2.rb

+# frozen_string_literal: true
+class DeleteInconsistentInternalIdRecords2 < ActiveRecord::Migration[5.0]
+  include Gitlab::Database::MigrationHelpers
+
+  DOWNTIME = false
+
+  disable_ddl_transaction!
+
+  # This migration cleans up any inconsistent records in internal_ids.
+  #
+  # That is, it deletes records that track a `last_value` that is
+  # smaller than the maximum internal id (usually `iid`) found in
+  # the corresponding model records.
+
+  def up
+    disable_statement_timeout do
+      delete_internal_id_records('milestones', 'project_id')
+      delete_internal_id_records('milestones', 'namespace_id', 'group_id')
+    end
+  end
+
+  class InternalId < ActiveRecord::Base
+    self.table_name = 'internal_ids'
+    enum usage: { issues: 0, merge_requests: 1, deployments: 2, milestones: 3, epics: 4, ci_pipelines: 5 }
+  end
+
+  private
+
+  def delete_internal_id_records(base_table, scope_column_name, base_scope_column_name = scope_column_name)
+    sql = <<~SQL
+      SELECT id FROM ( -- workaround for MySQL
+       SELECT internal_ids.id FROM (
+         SELECT #{base_scope_column_name} AS #{scope_column_name}, max(iid) as maximum_iid from #{base_table} GROUP BY #{scope_column_name}
+       ) maxima JOIN internal_ids USING (#{scope_column_name})
+       WHERE internal_ids.usage=#{InternalId.usages.fetch(base_table)} AND maxima.maximum_iid > internal_ids.last_value
+      ) internal_ids
+    SQL
+
+    InternalId.where("id IN (#{sql})").tap do |ids| # rubocop:disable GitlabSecurity/SqlInjection
+      say "Deleting internal_id records for #{base_table}: #{ids.map { |i| [i.project_id, i.last_value] }}" unless ids.empty?
+    end.delete_all
+  end
+end