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I engaged with the AWS support billing team to address this issue, Initially, they recommended purchasing AWS Developer Support to access developer assistance for the problem at hand. I expressed my belief that the issue is AWS internal, and they agreed to investigate further.
After a period of 4 to 5 days, the support team took action by deleting the NodeGroup, which allowed me to delete the EKS cluster.
I asked them a technical reason and this is what they replied:
This is an internal issue at the AWS end and this can occur due to various reasons. However, they've suggested you to wait till the current request is completed before you can submit next action. For example: When you create a Cluster wait for it to be successfully complete before initiating the creation of Node groups. If we avoid overlapping the requests while one is in progress we can avoid this error from repeating again.
I destroyed resources by terraform destroy, maybe issue occurred from terraform.
I would check if there are manual changes to the deploy so that terraform plan gets misaligned hence delete get stuck?
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