Sorry, But I figured out how we can do it. Just answering my question here so that will be useful for others as well.
We can do it using simple filesystem merge for directories but after that we need to make sure that we give appropriate permission to all files for vmail
user (user might be specific to zpanel).
This is what worked for me . Under /var/zpanel/vmail/my-domain.com/cur/
:
$ sudo chown vmail:mail *
Same we need to do for /new
and /tmp
directories.