When the app autoscale, the previous modifications made in first instance will be kept in new instances?
You will need to add configuration settings to your application archive so that each instance is configured the same way when it is brought online. This is done by creating a folder in your application called .ebextensions. You place files in that folder with the .config extenstion. These should be yaml format.
Check these docs for more information: http://docs.aws.amazon.com/elasticbeanstalk/latest/dg/customize-containers.html
Linux specific (I assume Linux since you mention SSH): http://docs.aws.amazon.com/elasticbeanstalk/latest/dg/customize-containers-ec2.html