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The AWS Security Hub integration with AWS Control Tower is in preview. Controls owned by Security Hub are not aggregated in the compliance status of accounts and OUs in AWS Control Tower. This is a standard warning on all accounts, but it means that if you enable a Control thats owned by Security Hub on an OU, and that control is non-compliant in Security Hub, Control Tower will still show the Account and OU as Compliant on the dashboard. That is why you receive the warning, you need to check both Control Tower and Security Hub for an accurate compliance status.
https://docs.aws.amazon.com/controltower/latest/userguide/security-hub-controls.html
I am also seeing this same compliance status warning and wondering what it means.
I ran into the same issue using AWS CT 3.0, wondering if you figured it out ?
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