The auto scaling feature of Elastic Beanstalk will automatically start another instance if a current instance continues to fail a health check. Stopping individual instances outside of the environment will cause failed health checks and trigger a new instance to be spun up.
You will be charged when the components within the environment are running as stated by Amazon here:
There is no additional charge for Elastic Beanstalk – you only pay for the underlying AWS resources (e.g. Amazon EC2, Amazon S3) that your application consumes.
You can completely stop an environment through the CLI. I gave this answer to a previous question about starting and stopping Elastic Beanstalk:
The EB command line interface has an eb stop
command. Here is a little bit about what the command actually does:
The eb stop command deletes the AWS resources that are running your application (such as the ELB and the EC2 instances). It however leaves behind all of the application versions and configuration settings that you had deployed, so you can quickly get started again. Eb stop is ideal when you are developing and testing your application and don’t need the AWS resources running over night. You can get going again by simply running eb start.