The Cathedral Ships weren't going just to give up because their leadership had been defeated in another layer of space. That wasn't how they operated and wasn't at all in their nature.
As soon as the defeat was noticed, they doubled down on their aggressiveness, trying to push back the combined force of the Morphos and the Humans while retaking the lost portions of the surface.
It wasn't going well, with the human vessels being vastly superior to them in firepower and shielding, but the numbers advantage was enough for them to at least hold on while the battle for the surface raged.
[Drone Bombers are away with the supply drops for the resistance. The Android Mecha force has stabilized the region around the motherships, and no more interceptors are currently detected.] The AI reported.