We have a MySQL server in one of the remote Virtual Machine (Windows Server 2008). Till yesterday we were able to connect to the MySQL server, with the help of workbench install
Chances are that your configuration was set up for an IP that has changed. By default, mysql won't let you connect from remote hosts unless you explicitly give permissions for a specific user on a specific schema or a group of schemas, for example if you did something like this:
GRANT ALL PRIVILEGES ON *.* TO 'USERNAME'@'1.2.3.4' IDENTIFIED BY 'PASSWORD' WITH GRANT OPTION;
Maybe what you actually did was to set the grant onto your own IP address, that is the address of your local machine, and if your local machine (not the remote server) has changed it's IP address, then mysql will not let you connect unless you have the "1.2.3.4" IP address which obviously you don't have anymore if you have a dynamic IP address (common with DSL/Cable connections)
So connect through SSH or Telnet or whatever you use to your windows server and go to mysql as root and do this:
SELECT * from information_schema.user_privileges;
That will show you the grants on all users and how they are allowed to connect. If you don't see your local IP Address listed there or a wildcard (which would allow you to connect from any remote machine to the server) then you have to set it up like this:
GRANT ALL PRIVILEGES ON *.* TO 'USERNAME'@'%' IDENTIFIED BY 'PASSWORD' WITH GRANT OPTION;
Where USERNAME of course is your user. See that after the on there is a wildcard / dot /wildcard that means you want that user to be able to connect to any schema (database, for mysql) from any user from any network. But I'd recommend that you only do the grant for the user for the specific schema you need to connect to.
Then after that, if you actually had the right information and still can't connect than use a portscanner like nmap or something like that to do a port scan and see if mysql is:
If 1 is true, then check 2 because maybe there is a misconfiguration of the port. But if any of these 2 points do work then it sounds definitely not like a network configuration but a user setting or something else.