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I've recently upgraded to the web dev plan. I've done the CNAME change to point my domain to my web app. Now I'd like to reclaim the original app slot (my~username.pythonanywhere.com) to develop something else.

Right now there is only one set of project files. If I make changes to it, it alters both my~username.pythonanywhere.com and the actual domain. How can I untangle these two?

If you go to the "Web" tab and select your yourusername.pythonanywhere.com app, then click the "Delete" button at the bottom of the page, that will disable the app. It won't delete the files (apart from the WSGI file, which I guess you copied over to your domain's web app).

You can then create a new web app in a different directory, and it will be independent.