GAE: Instance shutdown from source code
If can disable an entire application (from Application Settings page) for sometime and then reenable it (or you can delete it from that point onwards).
There is no way you can "shutdown" a particular instance. You can have different version of your application, but at any moment in time, you can only have only one instance as the active version of your application. You can however split traffic between different versions, but that does not change active versions.
In terms of performance, you can change the Max Idle Instances value to one so that only one of the instance is preloaded or active.
In user interface of Google App Engine, in "Instances" I can shutdown selected instances by press button "Shutdown".
Can I do shutdown by program from source code?