How to compare/Sync two database tables using Binary Search Or Any Faster Algorithms

Question

Hi
I have a requirement to compare two database tables(client/server - Synchronziation perpous) to sync client changes back to server. I selected both the database tables to DataTables and  
I used squential seach to sync/compare to database tables. Its working fine, but its its taking 9min to compare/sync to server. 9min is pretty slow, If any body implemented binary seach or any other faster ways to compare/sync database tables, Please suggest me.
 
Thank you,