I had logged into one of my customer's systems that has about 10 accounts, each running a Worppress Multisite setup with 25-75 domains on each account. For a particular email domain that was having issues, they were tied to a cert which was covering multiple domains. I didn't want to just UNinstall it and then hope to get AutoSSL to reinstall it without error / throttling.
so, I was playing around inside the actual cPanel interface, navigated to SSL/TLS, found the cert that had that domain on it and clicked on the option to Update Certificate. I clicked on that, then clicked Autofill by Domain, and noted that the new / proper CA bundle was in there already. I clicked on Install Certificate and it re-installed the cert and added all the email domains tied to that cert back into /var/cpanel/ssl/domain_tls and the incoming email SSL connections started working for those domains immediately. So I didn't even have to monkey around in WHM. Nice for this particular instance, where one hosting account has a bunch of certs, each with a bunch of domains on it.