I just went through the 'refurb' tango heading over to the UK on QF1/2 a couple of weeks' ago. As you noted earlier, when the aircraft were swapped to the refurbed aircraft, I lost my Y seat selections from the old mini-Y cabin down to the bottom - in both directions, even before I knew QF2 was a refurbed aircraft. I ended up in 86D going over and 85D coming back. I've now set a record in the office for the highest seat number. Our Sales Graduate is no longer complaining about getting 27D on a domestic flight.
I normally book FlexY and put in for upgrade to J. Over the past five years, in January I have got the upgrades in both directions and it's 50/50 for later in the year when I'm across to the UK (May & Sep). Not this time, and I didn't get notified until T-10 hours.
I didn't see any diiference in the Y seats, except that they have an extra mesh pocket below the main one in the seat back, which was handy for the water bottle and my cable bag.