When you bring the car in to VW, they will check to see what phases of the "fix" have been done by VIN, and what warranty is still in effect for the Gen 3 engine. If you have not had phase 2 done, the warranty directs them to replace the DPF at no cost to you, along with the remainder of phase 2 updates. A loaner car, per the emissions warranty, is provided. If your car has had phase 2 modifications but your manual transmission had under 70,000 miles, (and if) the DPF was not replaced at that time, and the warranty directs them to later replace the DPF at no cost to you (after 70k miles), and the DOC prior to the car reaching 150,000 miles. The warranty differs based on engine, and the documents linked above are helpful (especially if the dealership says they aren't familiar with the work).