I’m not exactly sure what’s happened, but the SSL cert isn’t on our system. I believe that we need to temporarily bypass the rate limit so that we can get the cert generated and installed.
I’m not sure honestly. I think cPanel might have glitched or something. We use AutoSSL on our cPanel / WHM servers and let that manage all SSL certs and vhosts.
Let's Encrypt will make rate limit adjustments when an organization has a large enough number of students, customers, employees, etc., who need separate certificates that would otherwise exceed Let's Encrypt's rate limits. But Let's Encrypt doesn't make adjustments based on an error or misconfiguration by an individual client or user that resulted in certificates or keys not being saved. AutoSSL might be creating a misleading expectation here.
You might want to talk to cPanel support to see if they can help you figure out how the glitch happened, in case it's a bug that affects other people.
In terms of the rate limit, your main options are
wait 7 days for this limit to time out
add or remove a subdomain (since the rate limit in question is calculated based on the "exact set of names", and will not apply if there are more or fewer names covered than there were in the original certificates)
use a different ACME CA like BuyPass or ZeroSSL instead of Let's Encrypt
find the certificates or keys somewhere on your system, if they might still exist somewhere