I recently changed my VPS hostname & the nameservers too in my whm panel. My question is, do I have to do anything in Cloudflare or all domains will be working fine. Note that I am using the Cloudflare provided nameserver in the respective domain’s register.
Greetings,
Thank you for asking.
Are you using Cloudflare nameservers at domain registrar, or rather on your VPS as “NS” type of the DNS record for your domain name? 
If the A type of the DNS records point to the same IP, I believe you’re good to go 
However, if that VPS is also used for an e-mail, kindly see the article from below in such case if you’re going to encounter some issue with receiving/sending e-mails for some domains and for tips related to troubleshooting.
Nevertheless, what I’ve got few times was I changed the hostname and cPanel got stuck because the cPanel Licence type was tied to the IP/hostname (bare metal dedicated server). Therefore, I had to do it via CLI to fix it. It’s not related to the Cloudflare itself, rather just adding it here as a case which I have had.
Furthermore, may I ask for each of the domains which are serving content from the same VPS or, just “main” or “sub” one which the VPS uses as a hostname?
- like
example.comis the domain name at your CF account andmyserver.example.comis the sub-domain, rather hostname of that particular VPS.
Also, double-check if your SSL certificates are valid and ok 
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