We moved from old server to new server. And I found few wrong configurations which was the reason for not moving images/files to target directories.
PHP-FPM was not enabled
Our site was running on PHP
PHP-FPM was not enabled on our website. So this means it was not using site specific
Wrong home directory
I mistakenly set home path for the sub-domains in cPanel. They were pointing to the sub-domain root instead of the
web folder ( in phalcon we have web as home directory ). So
$_SERVER['DOCUMENT_ROOT'] was pointing to the root folder; not to the