I do something similar in another application.  I load
the "new" data into another table with the exact structure
of the main table.  Then I use an update query to match
the records between the two tables and update the main
table with the new data.  The only thing I had to do was
to make sure I could create a key that is unique enough to
distinguish one record from another.  In one instance, I
had to concantenate several fields together to do this.

Hope this helps.