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The reporter tracked the data loss down to how the config files were written: Ruby's File.write modifies the file in place while refinery's live-reload reads it. Switching the deployment script to cp instead of File.write fixed it, and trace volume returned to normal in the graphs. If your live-reload config deploys are mysteriously breaking sampling, try switching the write to an atomic replacement and see whether the loss disappears.
Source: https://github.com/honeycombio/refinery/issues/384
Source: https://github.com/honeycombio/refinery/issues/384