So I'm looking at the seating diagrams:
For the 788, there is indeed a loss of J, however if you consider PE to be a premium cabin, there is actually a net of 13 premium seats, or put differently, 13 seats seats that are tollerable for an ULH flight. Granted, most of the PE cabin is ex J real estate, and the reduction of E+ is more attributed to the increase in Y.
For the 789, The current J capacity is retained plus an additional 21 PE seats, makes for 21 additional tollerable seats. However the E+ cabin was gutted for PE and some additonal Y seats.
Being a kettle myself, I'm not familar with the ins and outs of the upgrades and can't measure if the benefits outweight the cost of limited E+ seats for elites, however the general consensus (based of of FT posts) seems to be that E+ is still sub-par for these long trips.