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Accepted Answer
👋 @wesbos
As you may have guessed, the spec is a representation of your app, when updating without the environment variables we take that to mean the current env vars should not be included.
A possible solution is, when creating the environment variables mark the secret ones as secret and when you’re happy with this you can go to the settings tab and view the App Spec which will have encrypted values for your secrets. These values are bound to your app and can be safely stored in your git repository. You can also use this spec to update your app and the encrypted values will continue to work as expected.