Greetings,
Did you measure where your chunks were taking more time? It would be nice to know if it is the database inserts that get slower, or if it is reading the file that gets slower. The last time I did something like this, I created a .NET extension to read a file from up from a certain point (using seek) that returned a list of records to Service Studio.
Then i used this extension https://www.outsystems.com/forge/component/1117/bulkinsert/ to do batch inserts. If your table has indexes, disabling them during the insert and enabling them after may speed up your process.
If you also need to do updates, then you may want to consider inserting your records into a staging table and using MERGE (https://msdn.microsoft.com/en-us/library/bb510625.aspx), assuming you have SQL Server as your database. If you go the MERGE route, you may want to grant additional permissions to the OSRUNTIME user, so it can use TRUNCATE TABLE on the staging table.