Publishing over an existing published folder of the same name (as after making revisions), erases the contents
If you make revisions to a project that you previously published to a folder, and you re-publish over that same folder, it erases the contents of the folder and does not create new published content. You end up with a folder that only has the project.text file in it.
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Jeff McKune commented
The work around is to name your output folder something different and do not attempt to publish over a folder of the same name.