I see you have thought this one out. I would still like to suggest that you add a staging table and copy the data into it before processing, and then do all you processing in sql. This should avoid the issues as the database itself will be doing the comparisons, and with where not exists, at the same time as the insertion.
If there are multiple steps, a stored procedure can be used, or a series stored procedures called from another one, should you want separate entry points.
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