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The populator writes through its own store instances, so after the inline backfill the toolbox's store still served its cached pre-populate index. Single-instance that cache is merely stale-but-identical; on a shared database (the CI integration shards share one postgres DB, and any multi-server deployment shares one in production) the cached index is another instance's view and the eager walk drops every tool missing from it — the post-reload 'no index entry for upload.xml' cascade. Reload integration tests drive galaxy.queue_worker.reload_toolbox directly and reproduce the failure with a foreign index row; the earlier send_control_task-based attempts passed vacuously because the control message never executes in this harness.