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Yeah we have a few APIs like that too, they don't play well with the "assume an open world" assumption of KRM. We do our best to validate the state transitions in webhooks. IMO not being able to manipulate them is a feature. :P when we need to manipulate we set a field called `spec.paused:true`.
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That's a break-the-glass button to stop reconciliation. You unfuck the situation but then bring the config change back to the CRD long-term. There's not really a good way to keep reconciling with multiple SoTs. Brian Grant has great articles on the topic medium.com/@bgrant0607/...