Why is Cpanel restarting all instances of Mysql

the mysql restart given in WHM is for restarting the mysql service on the server itself, its same as doing a mysql restart from ssh.

it says "restart Services" not "instances"
if you see a hung mysql process you should kill that particular from ssh or from whm-->Show Current CPU Usage.

 

You are clearly quite confused regarding MySQL ....

There is only ONE MySQL server and only one "instance" as you put it running on your server --- THERE IS NO OTHER!

You could not possibly be running more than one MySQL on the same server and that would be unreasonable to even consider that though you could have both MySQL and PostgreSQL together the same server but that's a different service.

What you are thinking of and incorrected referring to as "instances" is actually child process of your one single solitary running MySQL server.

When you issue a "restart" for MySQL whether that be from WHM or SSH or anywhere for that matter, you are telling the MySQL server itself to restart which means the database server and all it's sub process will go down temporary for the restart.

What you are talking about is something parallel to like trying to reboot your home computer and then complaining that your Excel spreadsheet goes down. Yes, it's going to do that. :D