Before using the eb init command, make sure that you select an existing application and environment.
Settings created by eb init will be default setting for future environments and it won't overwrite any settings on the running environment.
As for the instances, they can be created and terminated at any time by Elastic Beanstalk, based on health and autoscaling policies. If your instances are healthy and no autoscaling event occurs then there won't be any replaced instances caused by eb deploy.