Were you able to figure out what was going on?
I had this issue yesterday and today, but I needed the changes applies ASAP and so did things through the back end: I had a clone of the site whose settings were exactly the way I needed them to be and used AGOL assistant to find and copy the relevant JSON snippet from the clone on to the original.
It's a bit of a risky option, as you could break things if you're not careful when modifying the JSON, but it did the trick for me.
