Since the issuance succeeded, do you have copies of any of the certificates (and private keys) that they created? Maybe the certificates are just sitting around on your hard drive but not being used by your web server?
For instance, if you use
certbot certonly (or any of the other names of the Certbot client with
certonly), then you obtain the certificate but don’t install it, so you still have to edit web server configuration files in order to install the certificate that you’ve issued. (Some system administrators strongly prefer this method because they’re accustomed to administering their web server primarily by editing its configuration files with a text editor.)
With Certbot you can use
--staging which uses the testing server, which doesn’t count against your regular rate limits. Other applications should have a similar method.
As an expert Let’s Encrypt user, I would use Certbot to issue a new certificate that covers the main domain and an additional subdomain in order to circumvent the rate limit.
As a novice Let’s Encrypt user, I would pick one particular Let’s Encrypt client application and try to make it work using that application. If it didn’t work, I would immediately ask on the forum about what the problem was, explaining which Let’s Encrypt client application I used, how I ran it, and what error messages, if any, I encountered. Then probably other forum users would help me debug the process. If I just switched to a completely different method every time I encountered a problem, even though the certificate issuance had already taken place, I would probably quickly run into rate limits…