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After going through the process to have my domain I purchased show a web app that I've already created (creating a new app and modifying the wsgi.py file), I'm wondering if I can now delete the old app.

As of now, I have two apps. username.pythonanywhere.com and www.username.com

Is there a way to safely delete the original (first) app and work on a new app?

Deleting a web app in the Web tab doesn't actually delete any code -- it just switches off the old website... So if your new app is up and running, just delete the old one and keep working on the new one...