You should never store anything valuable on ephemeral storage in Amazon EC2 instances. As ephemeral storage will be lost as soon as the instance is stopped. it's meant for the temporary data only that you can afford to lose.
You cannot take backups of ephemeral storage using the concepts of snapshots as they only apply on EBS volumes.
So in order to back up your ephemeral storage, you will have to use a regular operating system level backup tool of your choice that supports Amazon S3 so that you can keep your backup in AWS only