Certbot on Windows, with a specified CSR file, is almost certainly the hardest way of accomplishing what you're trying to do. The certbot team no longer supports Windows, and using a manual authentication with CSR will prevent automation. You probably want to use one of the clients designed for Windows, like Certify the Web or win-acme, to automatically configure your Apache-on-Windows installation and be able to renew automatically.
In terms of your actual error message, that's a pretty unusual one. It may be just a one-off fluke, which their staff calls "the 404 bug" of their replicas not being as synchronized as they're supposed to be. (And they had some challenges with keeping up with their load recently; I don't know if that might be related.) I'd suggest just trying again, and seeing if it recurs.