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<https://www.pulumi.com/docs/intro/concepts/resources/options/ignorechanges/>

So I guess I can use 1 stack with 2 node pools and when the updtae happens ignoreChanges on one pool, update the other and then stop ignoring them and updating the secon

what are you ultimately trying to achieve?

A resilient cluster which can survive updates to the cloudformation stack which include things like changing the ami- or the node types.
i.e. something where I can update the pulumi/eks module for different node pools at different times. Thus ensuring I can make such updates without downtime for my essential services.