Nature of Amazon EC2 Instances and Other AWS Services

I have some basic (dumb) questions about AWS EC2 instances or AMI.

I created a directory and some test file to check if the files are saved outside the stop and start instance.

When I go to stop my Ubuntu instance I get the following warning:

Are you sure you want to stop this instance? Note: Please note that any data on your instance's ephemeral storage will be lost when it is stopped.

But when I start the Ubuntu instance again, my test file and file still exist, persist. What is this warning about?

If I can install MySQL, GlassFish server, etc. to this instance, when will the need for Amazon Relational Database Service (RDS), DynamoDB, and Storage Gateway arise? Are these last mentioned AWS services for large enterprises that need more reliability and scalability, but not for private users who don't need a lot of storage?

Hm, my current understanding is that storing in EC2 instances is safe as long as (duh) I don't delete them, and data in RDS and Storage Gateway etc. will save the deletion of the instance. Assuming that as long as I have full control over the life of EC2 instances, I shouldn't worry.

Greetings.