I have just updated the latest virtualmin packages on my ubuntu. It requires to do post-installation wizard again which I completed. Without changing any settings from previous setup, using back previous mysql password. Will this affect my application that are running on the server?
Not if you don’t change anything. The only possibly risky thing would be if you changed the MySQL password and some other tools relied on the old password (but Virtualmin will sync up for itself, so it won’t break Virtualmin to change the database password).