As stated in the github document I linked to, the file should be in the root of the Github Pages website. You have configured github pages to use your Master branch, so the root is the folder above, the root of you project. They say
disable the Jekyll build process by creating an empty file called .nojekyll in the root of your publishing source
This is nothing with R or xaringan just how Github Pages is working.
But as you said, it has worked before even with jekyll used (which I still don't think you need).
So, you should check your actions panes in Github as there will be some information in why the run is failling. I don't see this a deployment for your last commit also:
Maybe check Github pages configuration in settings too.
Happy to help further but I can't see those pane for you.