I'm not sure what is really going on, but if you are inserting duplicates and updating Primary Keys as part of a bulk load process, then a staging table might be the solution for you. You create a table that you make sure is empty prior to the bulk load, then load it with the 100% raw data from the file, then process that data into your real tables (set based is best). You can do things like this to insert all rows that don't already exist:
INSERT INTO RealTable
(pk, col1, col2, col3)
SELECT
pk, col1, col2, col3
FROM StageTable s
WHERE NOT EXISTS (SELECT
1
FROM RealTable r
WHERE s.pk=r.pk
)
Prevent the duplicates in the first place is best. You could also do UPDATEs on your real table by joining in the staging table, etc. This will avoid the need to "work around" the constraints. When you work around the constraints, you usually create difficult to find bugs.