Cannot delete version

If you want to stop app engine you can disable it App Engine -> Settings -> Disable application

This will only stop traffic to you Application after that you can remove the instances.

You have to have at least one version for the default module. That's the reason why it doesn't allow you to delete it.

You need to deploy a new version, it can be a Flexible VM (deployed to another region in your situation), or Standard VM.

As a workaround, when you don't have any app to replace it right now, you can deploy an empty app instead. You have to create an app.yaml:

---
runtime: python38
handlers:
  - url: /
    script: auto

and deploy it using:

gcloud app deploy app.yaml

As your app.yaml doesn't have any script to execute, you'll not be charged for any instance.