Thank you Miguel for the clarification.
Currently the App Engine Flexible environment requires
at least one instance to be active in a version in order for requests to be routed to it. Our engineering team is working very hard on a good "scale to zero" solution for the Flex environment. There is currently no ETA for its implementation.
In the meantime, there is a great article on
Reducing Costs for App Engine Flex that I recommend you read. The idea is the same, reduce instances, but for every deployed version and service. When you deploy a new version on your app, App Engine will keep the instances of older versions running. This will in turn increase costs for every deployed version and service. You should therefore ensure to delete all instances in all unused versions.
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Concerning health checks. Health check requests to your application will not affect performance or cost. A health check will not ask your application to do any work, and instead simply pings the instance and container running your application to ensure they are alive and well.