Auto-scaling is designed to be used with "immutable" EC2 instances. Meaning, the EC2 instances under control of auto-scaling won't be changed or updated.
Data that is uploaded to such EC2 instances is usually saved somewhere off the instance (off instance database, S3 object store, etc.)
For software/application updates, you usually wouldn't update the EC2 instances directly. Instead, you have a process to create a new "master" AMI image. Once you have the new master AMI image, you update your Auto Scaling group to use the new image.
There are many available processes you can choose from to create your new AMI images.
All this being said, you can modify/update your EC2 instances that are under control of Auto Scaling. But this may only really work if your Auto Scaling group has a min = max = size of 1. Anything more than 1 and you really want to have another process to create your master AMI image.