Okay I was thinking about some thing how come the Enclave did not take interest in Liberty Prime in Fallout 3. I mean he is a super weapon they must of had files about him some where he was one of the most important projects during the great war. If indeed they had files on him and knew he was in the Citadel / Pentagon where the Brother Hood is why not just destroy the Citadel with an oribital strike and kill 2 birds with one stone destroy the Brother Hood and Liberty Prime then they could work on project purity without the Brother Hood getting in the way.

Some secrets are only allowed to be known by a select number of people.
My guess is that wherever Lyons Brotherhood found it, the people who knew of it prior to them, pre-war, had all died.
Just cause they're part of the government, just cause they might have the president and all that, doesn't mean they have every secret available to them.

A. Fallout 3 has plotholes, this is one of them.

B. The entire might of the pre-war government and Mr. House couldn't get Liberty Prime to work right. If they did have records and knew that it was there, they probably thought it was worthless. How Dr. Li, a wasteland scientists who plays with fresh food, was able to get Liberty Prime working is beyond me.

C. Perhaps the records in Raven Rock were incomplete on where Liberty Prime was. Or it was listed as "project cancelled" or something along those lines.

D. The Bradley-Hercules wasn't working apparently until after the battle at the purifier. After the battle and during the events of Broken Steel, no one really knows why the Enclave didn't just blow up the citadel. This again, is a plothole.