Google App Engine not updating deployed files

Make sure that before redeploying your APP after making changes you Remove Launch and Remove All Terminated launches by pressing the double cross buttons next to the "clear console" buttons on the console window in Eclipse...I hope this solve your problem.

In the logs, make sure that you're checking the correct version:

Otherwise redeploy to a brand new version and check that version explicitly directly from the version url that can be found under the Versions section.

I had a similar problem recently, and that I fixed by logging into appengine.google.com>MyAppIdentifier>(Main)>Versions and selecting the current version as the default.

This should not only serve your latest version, but also use the latest version for log viewing and other administrative tasks.