Anything that is not stored on an ebs volume that is mounted to the instance will be lost. For instance, if you mount your ebs volume at /mystuff, then anything not in /mystuff will be lost. If you don't mount an ebs volume and save stuff on it, then I believe everything will be lost.
To be clear and answer @Dean's question: EBS-type root storage doesn't seem to be ephemeral. Data is persistent across reboots and actually it doesn't make any sense to use ebs-backed root volume which is 'ephemeral'. This wouldn't be different from image-based root volume.
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