Did the dev team ever make changes to try and fix this? Your post is four years old, but I just ran into the same problem.
Somewhere my theme app extension and a colleague’s copy messed up the app proxy and I just spent hours trying to get it to work again. Removing the settings via the website, pushing new ones via my app.toml, refreshing, using other urls etc. In the end the only fix was to uninstall both apps and install my app again.