Hey help can't be provided based on what you provided. Typically you'd need to share a project with a minimal reproduction (i.e., get rid of anything that isn't about the issue you are trying to solve).
Sounds pretty advanced though and a lot can be going wrong.
This is exactly the same project present on github, I ran it in my terminal. I created a test project as you can see in the video I put a favicon and two html scripts one in the custom code and the other in the main page and when I publish the project there is no modification it seems that something limits this. Before I tested by putting scripts like that it appears for a second and disappears just as quickly. I wonder if it is that there are restrictions in the project itself?
