Delete from the target table where the same data exists in the source table.  At this point if the source row = target row its ok.  If source row has updated values you dont care either becuase the next step is to insert all source rows to the target which is essentially overwritting rows that have been updated within the source.

The easiest way of all however would be to use some kind of auditing within you loads from source to target.  But we dont live in a perfect world. 

If I could VPN to a client site I would add a sample package but again, we dont live in a perfect world!!!!!