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The easiest way to stop your CloudShell data from being deleted - although as @Riku_Kobayashi correctly says, even if it is deleted it won't touch any data already in S3 - is to open it up and use it https://aws.amazon.com/cloudshell/faqs/#Limits_.26_usage
Q: How can I prevent my CloudShell storage from being deleted?
Sign in to the AWS Management Console and open CloudShell in the expiring Region. This will reset the time associated with your storage in the given Region.
Hello.
Even if CloudShell data is deleted, the data uploaded to S3 will not be deleted.
For example, if you have data that has not been uploaded to S3 yet, I think it would be a good idea to sign in with the relevant IAM user, access CloudShell, and then upload it to S3.
https://docs.aws.amazon.com/cloudshell/latest/userguide/limits.html#persistent-storage-limitations
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Great thank you for confirming!