Letsencrypt - make sure that your site is pointed to same server

I am using easy engine with letsencrypt since 4-5 months never faced an issue.

I transferred a site from other server to easyengine. and when I use ee site update command to get letsencrypt it says

“Unable to setup, Let’s Encrypt
Please make sure that your site is pointed to
same server on which you are running Let’s Encrypt Client
to allow it to verify the site automatically.”

But the site is already migrated and pointed using A record and its working. I am able to open the site and work.
But when it comes to issue letsencrypt certificate it shows error.
I tried to generate the certificates manually but still got this error.

Make sure that both the root domain and the www are pointing to the server… Check the website error logs for more info. Let me know if this helps!

I have already checked that both www and . domains are pointing to my server Ip. I think the issue is within something else. Still to find the real cause.