What it says on the tin. The part that normally appears over the right nacelle (or top right for quad-nacelle ships) when the Assimilated Subtranswarp Engines are equipped to the Peghqu' Heavy Destroyer appear instead merged into a part near the parts that move to allow for the Disruptor Lotus.
This piece should be on the right nacelle of the ship, as it is on all other ships that I have seen it on. (It would also be great if the graphic for both nacelles and impulse engines applied multiple graphics for ships with more than one-two impulse engines and/or more than two nacelles, such as the Heavy Cruiser, Advanced Heavy Cruiser, and Advanced Escort.)
As for the impulse engine graphic and deflector array graphic provided by the parts in the Borg set, kudos to whoever did the work on placing them on the model for the Peghqu', as they meld beautifully into the ship's design. The deflector array graphic is even resized to fit the ship better, which is something that other ships don't have because that graphic tends to stay around the same size on all other ships.