It is not recommended to change the code that is currently running on a single App Engine instance. Since
App Engine scales its instances of your application, that single instance may turn down due to low traffic, and you would lose any changes persisted on that instance. Likewise, new instances created due to higher traffic will not posses the change you made (since it was only local to that single instance). Additionally you cannot control which instance a request will run on.
It is therefore recommended to directly
deploy a new App Engine version with your code change, and then
migrate your traffic to the new version. This way no requests will be made to your new version until you deploy it and/or migrate traffic to it (as deploying may actually migrate traffic for you automatically). Once deployed, all requests will now see your configuration change and run on the new code.