The EFF develops Certbot (not ISRG who does Let's Encrypt). EFF dropped support for Certbot on Windows this past Feb.
Certbot was never the best ACME Client on Windows although certain cases it worked okay. Certify the Web and others were designed for Windows. Certify being easiest but win-acme and posh-acme also have their place. See: ACME Client Implementations - Let's Encrypt
You used to have a cert with both your apex and www subdomains in it. But, the -0001 only has your apex. I'm not sure how you got in the state you did. Normally running Certbot renew just updates your existing certs. To get a -0001 means you must have tried to issue a new one. Without knowing exactly what you did it is hard to say how to proceed.
It seems a good time to migrate away from Certbot rather than repairing a mixed-up config.
Certify is extremely well-integrated with IIS especially and is a nice gui. It would probably be very easy to migrate to.