I think I can see that you are not very familiar with MySQL and its internals. MySQL is a server. You access it through a client (like SQLyog). The server will handle the file where data are stored. The client will not – it will send SQL statements to the server 'instructing' teh server what to do. Also you (as a human user) should not manipulate the databse files. It is only safe to let the server do.
You can sync databases in SQLyog ENTERPRISE and ULITMATE. The options is available from the 'powertools' menu.
Please
1) Download the TRIAL from http://webyog.com/en/downloads.php
2) Study the program documentation (help .. help menu)
3) Refer to our FAQ for specific issues: http://webyog.com/en/jobs_at_webyog.php
And besides there is the MySQL documentation: http://dev.mysql.com/doc/