What I would do is;
Add a look-up transformation to look-up against the destination to see if the data exists, If you have a primary key you can join on this or you could join on the filename if you are saving it.
Then I would add a conditional split that would split out the data returned from the look-up and dump all the records that have data as this would indicate that are already in the table. I would put these rejected records into a table or data file so you can check double check the logic.