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When you mention there's nothing in the logs around the time that the instance check fails, does this mean you can still login to the EC2 instance and look at the logs while its status is failed? Or are you having to restart the instance and then look back at the logs from the time of the failure?
Troubleshooting suggestions are here although it sounds like you have gone through a lot of them before posting your question https://repost.aws/knowledge-center/ec2-linux-status-check-failure
And here https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/TroubleshootingInstances.html
I note what you say about resource exhaustion not appearing to be a factor, it would still be worth putting CloudWatch Agent on the host to get a more detailed view of resource consumption https://docs.aws.amazon.com/AmazonCloudWatch/latest/monitoring/Install-CloudWatch-Agent.html
What is the instance type, and what sort of workload is it running?
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