Basically, root volume (your entire virtual system disk) is ephemeral, but only if you choose to create AMI backed by Amazon EC2 instance store.
If you choose to create AMI backed by EBS then your root volume is backed by EBS and everything you have on your root volume will be saved between reboots.
If you are not sure what type of volume you have, look under EC2->Elastic Block Store->Volumes in your AWS console and if your AMI root volume is listed there then you are safe. Also, if you go to EC2->Instances and then look under column "Root device type" of your instance and if it says "ebs", then you don't have to worry about data on your root device.
More details here: http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/RootDeviceStorage.html