I run several hosting servers based on cPanel software.
The problem occurred after the new updates, where it was withdrawn by cPanel certificate provider Sectigo.
In cPanel, each account defaults to account_name.domain_company.com.
Let's Encrypt, due to its limits, does not always want to renew the certificate for the account's root domain, by using the company domain name with each domain (and there are about 1,000 accounts and thus domains).
Due to the operation of my system, it badly needs the SSL certificate to be renewed for these domains.
Is there any chance to increase the LE limits for a specific domain?
Or any other workaround?
Are you saying that you operate example.com, require certificates for client-1.example.com through client-1000.example.com, and are running into the 50 Certificates per Registered Domain rate limit on example.com after switching to LetsEncrypt?
Short of a ratelimit adjustment, some options are :
use a wildcard certificate
use a load balancer in front of your system and terminate SSL on that, with 100 domains assigned onto each certificate.
purchase additional toplevel domains
However, if your concern can be read as the following - you have other issues:
You operate example.com which hosts a platform other companies CNAME onto. You require 1000 certificates for account_name.client-company-1.com through account_name.client-company-1000.com, and are running into various issues due to Rate Limits against a client's domain (such as client-company-1.com or client-company-1000.com)
In that scenario, you would need to host the system under your own subdomain and coordinate with your clients on when to procure a certificate.