WHMCS provide auto upgrade option in admin area. Here is now i upgrade my WHMCS installation. Steps are specifically for my install, posting for this my own future reference. You may need to modify the steps to suit your installation.

Before Upgrade

First backup WHMCS database

mysqldump hon_manage > hon_manage_before_upgrade-`date '+%Y-%m-%d-%H:%M:%S'`.sql

Set file ownership to www-data for web servers to update the files.

chown -R www-data:www-data /home/manage.hostonnet.com/public_html/

Update

Now login to WHMCS and do the upgrade.

After Upgrade

Change file ownership back to user root, so no one can change files. This is for safely, web server user can’t change any files even if WHMCS have a vulnerability.

chown -R root:root /home/manage.hostonnet.com/public_html/

Lets do some theme updates, so proper logo is displayed.

To change Admin logo, run

sed -i "s/templates\/{\$template}\/images\/logo.gif/https:\/\/s3.amazonaws.com\/fwcdn\/whmcs-admin-logo.png/g" /home/manage.hostonnet.com/public_html/honadmin/templates/blend/header.tpl

For customer area logo, edit file

vi /home/manage.hostonnet.com/public_html/templates/six/header.tpl

Find

<a href="{$WEB_ROOT}/index.php" class="logo"><img src="{$assetLogoPath}" alt="{$companyname}"></a>

Replace with

<a href="{$WEB_ROOT}/index.php" class="logo"><img src="https://s3.amazonaws.com/fwcdn/hon-white-logo.png" alt="{$companyname}" /></a>