Insert a New Line on an Existing Purchase Order

Background: We are currently working on an integration to hook up a legacy system with Netsuite Suitalk API. We were able to get inserts, updates, and upserts working just fine. We are using C# sdk and upsert operations. We are also providing unique external Ids and line id on each transaction...

Use Case:
Time 1: Create a Purchase Order with two Purchase order lines. (Works)
Time 2: Update a Purchase Order with two Purchase lines. (Works).
Time 3: Upsert a line 3, completely overwrites lines 1-2 (Bad)

We can't have that because there may be existing data attach to lines 1- 2. We expected the third line to be inserted into the database not affecting lines 1-2. Currently in the UI, you can do this. You can enter a purchase order then add additional lines. Am I using the wrong operation?