You need to drop the specific tables and then source in the new db files that will recreate the database files you just dropped. Be carefull to only drop the ones that you'll replace or you'll hose your db. (did that a few times lol) Open your new file in notepad and see what it creates or adds etc to know what to delete.
I usually use the mysql control center just cause i'm not fast with the cli yet, you might want to play with that, it helped me understand what I was doing a bit more. Still learning <grumble grumble>
-Nil
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