I've created two certificates - the productional and the stage one.
I've deleted stage one, however, it recreates itself and from time to time it sets itself in the page binding. Then I got problems with certificate validation as it's a stage, not the prod one.
Having IIS and certbot is an unusual combination, you'd usually need some sort of custom scripting in there to take the certificate from certbot and install it in IIS. And that may be where whatever problems you're seeing are arising from. Can you say more about how you've configured certbot? Or maybe at least the output of certbot certificates?