This post applies for a go based website deployed in appengine. It should work for other appengine based runtime's as well, but my configuration is with go runtime.
I deployed my website in appengine and, when i updated it later, my updates didn't reflect. After looking into the logs, i figured out that updates should be deployed with new version information in the app.yaml file. Check for the version tag and change it. But when you want to run the new instance, you have to prefix the version information before the url.
For example if your url is foo.appspot.com then for 'v2' of the appengine instance it should be v2.foo.appspot.com.From the appengine dashboard you can configure the version of the instance to be served by default and other options. Enjoy your time with appengine.