I've seen several posts here about breakpoints not working but they are all several years (and versions) old.
I had been using Pycharm 2018.3 for a while and decided to upgrade to 2019.3, the first launch copied settings from my existing 2018.3 ones and breakpoints now don't work on the same project.
Opening again the same project in 2018.3, breakpoints work again.
No configurations manually affected, just the upgrade has it ignoring breakpoints.
The breakpoints inside the same test work, but when using a webserver (cherrypy) the breakpoints inside server code stopped working as described above.