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my suspicion here is that the coredns deployment never starts because it’s not tolerating the fargate nodes

You are correct. The default annotation has a compute-type: ec2.
But ... well isn't that why the kubectl patch is run in the first place?

hmm yes. can you open an issue in <http://github.com/pulumi/pulumi-eks|github.com/pulumi/pulumi-eks>

the only WA that I found  which is really weird is to do a pulumi up with `aws.eks.Addon` then delete the coredns addon resource, then do a pulumi up again ???