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Hi there.
AWS Backup works by creating snapshots of your instances, therefore, it should be able to accomplish the task even if the instance is shutdown. The only problem might arise if while performing a backup the instance is terminated.
I hope this helps.
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As long as The AWS Instance Scheduler is only shutting down instances and DBs, then the backups should commence as planned. If the instances get terminated, then the backups will not be possible.
You should also be able to verify this behavior by shutting down an instance for 2 hours and verifying that the backups are still happening.