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
Mayank,
This behavior is something I see with every project. It is easy enough to work around by always saving to a different name, rather than overwriting.
Yes, my projects are saved in Dropbox. I just tried publishing to a local drive, and I got a "Replace?" warning dialog. I had to click the Replace button a couple of times, but it did go ahead and overwrite the files as expected. So this appears to be related to Dropbox or the use of a personal cloud storage service. Thank you!
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Hi Jeff,
This can be specific to the project or environment. Can you help me with the below?
1. Is it happening with only specific broject or all the projects? Can you create a sample project and test.
2. Is your project saved on any cloud like Onedrive or icloud? If yes then can you publish to local drive and replicate the issue?
Regards,
Mayank -
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.