Stop worrying about your server.
cPanel/Plesk Server Management for just $59/mo with Unlimited tickets, Unlimited admin hours, Security audits, 24×7 monitoring and lot more
In case MySQL database is showing fine under /var/lib/mysql but mission under cpanel database, its because of issue with database mapping.
Run these command from shell to fix it
Monthly server support with Unlimited tickets, 24×7 monitoring, Security Audit and lot more for just $59