I have now the opposite issue.

After setting the "breakpoints" custom prop to empty, execution still stops at the line where a red dot once lived before the reset. There is nothing there, and execution will continue properly if I set it going again, but it will stop each time I run the handler. An invisible red dot.
You have to be careful what you wish for. "Clear all breakpoints" fixes that, so I will change my tool as you pointed out. But weird, eh?
Craig