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I'm also interested in this but I couldn't find a way to do it natively. If you can programmatically get the kubeconfig you can probably do it via the kube client libs. My use case is patching coredns to run on fargate.

Yes, I was thinking something similar. This is going to be my approach:
• I'm going to use the official python k8s client to delete the original `aws-node` installation (ClusterRole, ClusterRoleBinding, ServiceAccount, etc)
• I found an official helm repo with <https://github.com/aws/eks-charts|multiple EKS related charts>. I'm going to use pulumi + helm to install the `aws-vpc-cni` (a.k.a `aws-node`) chart. I hope using this installation method give me more flexibility for future upgrades.