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When one uses an external metric provider for the metric templates, changing the secret can only be done by deleting and recreating the canary object, which in turn results in the deletion of the target object (and related pods).
Proposed solution
The external metric provider secret should be decoupled from the canary object, to allow one to make secret rotation or just plain changing the secret.
Any alternatives you've considered?
Maybe mount the secret in the flagger pod, when one deploys it as a replicas, a rollout has no impact.