I hope that if this is indeed the Lyon's Brotherhood, then Liberty Prime is still destroyed. They try to fix the insanely expensive pre war project using sensor modules, and cameras. I will be very upset. if towards the end of the game, if there is a final assualt on the Institute, right before you and your friends are destroyed by some super powerful weapon created by the Institute, all of a sudden Liberty Prime comes out of the shadows and destroys it, and helps you finish the fight.