Since I was not able to generate certificates from the aapanel, due to limit being reached [The signing failed, the current server IP has reached the limit of creating up to 10 accounts every 3 hours..].
So that I had used this website [https://www.sslforfree.com] for generating FREE SSLs and then verifying either via manual file verification or DNS verification. This helped to renew all certificates for websites hosted on aapanel, but I am unable to use the same certificate on aapanel's sub-domain. It does not apply SSL there, instead shows a message: SEC_ERROR_UNKNOWN_ISSUER.
PS: Cert started to work after some time automatically.
But auto-renewal is not working on aapanel, maybe that's due to cloudflare DNS usage, instead of using aapanel's own DNS.