This is expected behavior. If you deploy a version that specifies the same version ID as a version that already exists on App Engine, the files that you deploy will overwrite the existing version. This can be problematic if the version is serving traffic because traffic to your application might be disrupted. You can avoid disrupting traffic if you deploy your new version with a different version ID and then move traffic to that version. Related detail is offered on the "Deploying a PHP 5 App" documentation page <https://cloud.google.com/appengine/docs/standard/php/tools/uploadinganapp#deploying_an_app> .
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