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Prior, if the VirtualNetwork field on status was empty, it was assumed that network fields were not provided. The controller would then generate them. The VirtualNetwork field is always empty at the beginning of an EKS cluster being created regardless of if the network fields are provided or not. This caused the controlplane and nodegroups to use subnets belonging to different VPC's. This is invalid and causes an error. Now, the provider is determined by evaluating whether subnets have been provided or not. Also, nodegroups will now use the networking fields on status which should match what the cluster is using.
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