"Emissions Modification Phase 2 :
(available beginning in early 2018 )
The second part of the emissions modification will involve outfitting your
car with new emission control parts to ensure system reliability and
durability over time. If your car exceeds 40,000 miles (for automatic
transmissions) or 70,000 miles (for manual transmissions) we will install
updated emissions control system hardware - specifically a new Diesel
Particulate Filter, Diesel Oxidation Catalyst, and Selective Catalytic
Reduction Converter - that is needed to maintain emissions
performance for the full useful life (150,000 miles) of your vehicle. As
part of the Phase 2 modification, we will also install a second NOx
sensor and corresponding software to improve the performance of the
OBD system. The Phase 2 updates are expected to have no further
impact on overall vehicle reliability, durability, fuel economy, engine
sound, performance, or drivability.
You will receive a notice when Phase 2 of the emissions modification is
available for your vehicle. You should expect to receive this notice
before June 30, 2019. If your vehicle has accumulated fewer than
40,000 miles (for automatic transmissions) or 70,000 miles (for
manual transmissions) at the time of your Phase 2 update, your car will
need to have the Diesel Oxidation Catalyst replaced a second time,
before it reaches 150,000 miles. We will notify you when it is time to
bring your car in for the second catalyst replacement."
We'll have approx 15K on the clock, which from what I'm reading means just another software update and maybe a second NoX sensor, not all new hardware. Now we will need new hardware once they fail later on at 100K or what ever but it'll be covered (fingers crossed) under warranty.
From what I've read, the flash counter will be incremented but once it back to stock tune, all parameters will be stock. Only those pesky dealers that track flashes would notice the counter.