Just got a new update file from one of my suppliers. The have discontinued 904 products. How does the ECT csv import handle this scenario? say i have 30 qty in stock of one item in the list but out of stock on the rest of the items?

So if I understand correctly, you have some stock left you want to sell, so you do not want to use the suppliers stock level on that.
What you might try is download your stock levels before uploading the supplier changes.
Then upload the supplier changes, and after that, clean up your downloaded stock csv by removing the products that you do not want to alter, and upload that file back to set the stock on the ones you have some inventory left.

Personally I use some code I wrote to handle this kind of thing and if you are stuck, I may be able to help.

David