Reduce scope of orphaned builds to be removed

db/migrate/20180420010016_add_pipeline_build_foreign_key.rb

@@ -13,7 +13,7 @@ class AddPipelineBuildForeignKey < ActiveRecord::Migration
     execute <<~SQL
       DELETE FROM ci_builds WHERE NOT EXISTS
         (SELECT true FROM ci_pipelines WHERE ci_pipelines.id = ci_builds.commit_id)
-        AND commit_id IS NOT NULL
+        AND stage_id IS NULL
     SQL
 
     add_concurrent_foreign_key(:ci_builds, :ci_pipelines, column: :commit_id)