This application does not exist (app_id=xxx)
The same problem occurs with the Java/Eclipse plugin version of App Engine. The 404 happens when you're logged in to the wrong Google account from within the plugin. In that case, look at the bottom-left of Eclipse to see what account you're currently using.
Regarding the Python command line updater, if your cookies indicate that you're logged in to a Google account that doesn't have access to the application you're updating, then that would explain why ignoring those cookies by using "appcfg.py update --nocookies" fixes it.
I was unable to upload to an AppEngine as appcfg was telling me :

This application does not exist (app_id=u'xxx').

I was only a developer on the AppEngine, so as I was just testing I created a new AppEngine where I was the owner but I still get the same message on a newly created AppEngine.