If you are using autoscaling, instances will be terminated if they become unhealthy. In order to use autoscaling effectively, you should not keep any persistant data on the instance itself. This is called Shared Nothing architecture.
What you want to do, is create an AMI that has all your application and or tools to bootstrap your application. You would use this AMI as part of the launch configuration for your autoscale group. So if a new instance gets launched, either due to failure or needing to scale, your application will be back up without any interaction from you.