I am currently running a WHM instance on a VPS under subdomain.domain.com. The domain's main website is hosted on AWS, and the A record in cPanel points to that server instead of this one.

The nameservers for cPanel clients are issued by WHM and set to ns1.domain.com and ns2.domain.com.

I am planning to transfer the DNS from domain.com to CloudFlare and change the nameservers to CloudFlare. For ns1. and ns2., I will set up A records with the WHM IP and submit glue records at the domain registrar.

Is there any potential issue with day-to-day operation, including AutoSSL for the server hostname?

The reason behind this move is my desire to have my website on different infrastructure. If a client gets blocked out of the server or it goes offline, they would still be able to access my website for assistance.

As long as you ensure that the A records for ns1, ns2, and subdomain.domain.com are pointed to the correct IP address without proxying them, you will not face any issues.

Transferring your DNS to CloudFlare and changing the nameservers may introduce some potential issues with day-to-day operations, including AutoSSL for the server hostname. Here are a few considerations to keep in mind:

1. AutoSSL: When you change the nameservers, the AutoSSL process may be affected temporarily as it relies on the DNS resolution to issue and renew certificates. Ensure that CloudFlare properly handles SSL certificate validation during the transfer process.

2. Glue records: Setting up A records with the WHM IP and submitting glue records at the domain registrar should ensure seamless DNS resolution for your subdomain. However, ensure that the glue records are correctly configured and propagated across all the necessary DNS servers.

3. DNS propagation delay: Keep in mind that DNS changes can take time to propagate globally. It may take anywhere from a few minutes to 48 hours for the changes to fully propagate, during which some users might still be directed to the old DNS servers.

4. Server availability: While moving your website to a different infrastructure will provide redundancy, it's important to ensure that you have appropriate failover measures in place. Make sure your new infrastructure is capable of handling traffic in case the current server goes offline.

Before making any changes, it's recommended to thoroughly review the dоcumentation provided by CloudFlare and consult with their support team or a qualified system administrator to address any specific concerns related to your setup.

Relying on WHM's AutoSSL while changing nameservers is a gamble; if anything goes awry, your clients could be locked out of their sites, and the main website could become inaccessible. This setup doesn't guarantee redundancy; it only adds layers of complexity.
You may want to rethink this strategy—ensuring that your WHM hostname remains functional should be a priority, or you might end up in a mess of broken SSL certificates and angry clients.