We don't know, honestly I always assumed the worst; Lost Hills isn't a secret place really and, as the hub of the Brotherhood of Steel, I can't fathom a reason why the NCR won't be targeting it. The war has only been going on for a few years though right? The NCR will get it eventually, the Brotherhood are on the run.
Mr. House talks about a number of Brotherhood bunkers falling to the NCR, I think it was six or so. It is safe to say they are on the losing end of the War. What would remain of bunkers and chapters in the Core Region are probably on their own. "Look to your own defences" type deal. The NCR in New Vegas acted like it was already won to me.
No word on Lost Hills but as The Enclave said it is far from secret. Hopefully it is still around, a place that that shouldn't fall without any word of it.
They aren't on the run, given what we know know about Lyons and his mission to find tech as far as DC as well as other side missions.. He would have been sent there in the hopes he would discover a wonder weapon or a large cash of other conventional weapons to bring back to the Core Region because they say the writing on the walls. Maybe they discovered info on Optimus Prime and sent Lyon's to find it. That the tide was turning against him. Would also explain why they sent Arthur Maxson to live with Lyons, to be 3000 miles away from the NCR.
I agree, no mention of Lost Hills to me means that the Brotherhood must still have some power left, but I would also imagine that if Lost Hills is alive, it isn't doing well. What bunkers that haven't already fallen would be cut off from Lost Hills, just like how the Mojave was cut off from it.
All signs point to them being on their last legs, but I don't believe they are completey gone in the Core Region.
The way I see it things would have started going down hill after John Maxson's death which would have been sometime after Fallout. The other High Elders would have taken control and John's son might not have been that great of a leader or simply to young and later died leaving only Arthur Maxson and he is far to young. (Pretty sure there was another Maxson after John but before Arthur's father)
Then the debate came up about letting in outsiders, the minority that wanted change lost the vote and the elders sent them off on a mission some predicted would fail and it did. I see that as winning a civil war without firing a single shot.
So with the minority being eliminated, anyone left wanting change would have simply shut up about it, letting the more hard-line isolationists cement their power over the Brotherhood.
The Codex becoming the holy word if you will. When ever a question comes up they go to the codex and if the codex doesn't have an answer, they consult the codex thus creating an endless circle. Without a Maxson, there would be no one with the authority to change it and the hard-liners would not want to change it.
But those wanting change like Veronica that weren't sent a way formed their own groups, possibly arranging for Lyons to be the leader of the mission to DC and then later arranging for Arthur Maxson to be sent to DC, possibly with the hope that with Lyons he would learn new ways, such as letting in outsiders and someday return and take control of the Brotherhood of Steel and make serious reforms.
Maybe that was the true reason for Lyons going to DC, to get far enough a way from the main Brotherhood, but they couldn't have everything their way, hence the Outcast coming along.
The part of their mission about finding the MWBoS could have been them trying to find possible allies, but instead they discovered that the MWBoS changed far to much, becoming a facist military state. After all over 90 years had passed without giving a crap about looking for them and out of the blue someone said "oh hey see if you can find out about the airconvoy we sent out 90 years ago with a good chunk of the Brotherhood on it" It just doesn't make sense, unless they were hoping to find like minded people to join up with.
Lyons and his guys found Liberty Prime pretty much on day one of doing to DC and that was 23 years before Fallout 3 takes place. The problem was that Liberty Prime didn't work, if the orginal BoS thought it was so awesome the Outcast would have stayed. But all the info on it said it wasn't going to work and had problems.
Arther Maxson was not sent with Lyons. Arther Maxson was sent to Lyons several years after Lyons had already set up shop in DC using the Pentagon as his base. So this would mean that the orginal Brotherhood and Lyons group had regular contact with one another for several years by sending people back and forth between Lost Hills and the Citadel.
Lyons and Rothchild talk about how over time the orginal Brotherhood got tired of Lyons dragging his feet on his mission and helping wastelanders.
http://fallout.wikia.com/wiki/Arthur_Maxson was born in 2267 and sent to DC after his parents were killed in the Core Region. Fallout 3 takes place in 2277, making Arthur 10 years old.
http://fallout.wikia.com/wiki/Owyn_Lyons was sent to DC in 2254, so that is 23 years before Fallout 3 takes place.
So that means Lyons and his people were in DC for 13 years before Arthur Maxson was even born.
So there could have been people in the Core Region seeing what Lyons was doing and thought it would be a good idea to send Arthur there to learn, before the Elders finally got pissed enough at Lyons and cut him off. The official reason for sending him would be to keep him safe and we know now it would be because of the war with the NCR.
Damn Styles. You make a good point.
I always thought maybe they sent Arthur away as well due to the tensions between the NCR and the BoS.
A figure head like Arthur being captured and held hostage could possibly give the NCR the upper hand in diplomatic speakings.
Hence why the WCBoS could be ignoring them. Pretending they don't exist, so if the WCBoS were to be taken over, they still wouldn't have Maxson, and there would still be remnants of the Brotherhood safely out of reach of the NCR.
My theory at least.
Thans
Fallout 3 to me makes it clear that the West Coast Brotherhood just got tired of Lyons wasting time helping people and not doing the mission he was sent to do, he was given over a decade to follow his orders before the Elders back West just said to hell with him.
If it was more of a "Ok we are going to hide you guys in DC incase we are wiped out" type deal, I would think they would let Lyons and his guys in on it, to prevent something like the Outcast from splitting off.
Given the Brotherhood NCR tentions, I can see the Elders back West being more forgiving of Lyons and his ways, but as the War got started (we don't know when it started) and the BoS started losing, I would imagine the Elders back in Lost Hills really started losing their minds over Lyons dragging his feet. As in "We are losing a war and that guy is messing around with a busted water purifier! " So they would have just said "to hell with him."
And I theorise, the Hard-liners back in Lost Hills wouldn't really care or recognize Arthur Maxson as their leader, at best a figure head, a ten year old figure head. So him being stuck in DC is no skin off their nose, the last of the Maxsons gone and they can have total control, which I believe they already had but no more "figure head."
John Maxson wasn't a dictator, nore was his father or Roger Maxson. They were the top dog for sure, but there was also a council of Elders and without a Maxson to be "king" the Elders took over the role of leadership and I believe this happened sometime after Fallout after John died. There were still Maxsons but there could be a number of reasons they never ended up being top dog, like Arthur being only a child.
Perhaps they should have told them. Would make more sense.
Though what I don't understand is, even though they may dislike Lyons and all that, why wouldn't they tell them they are in a war with a very large foe, so maybe they should get their asses moving, and help them out. I mean, if the Enclave weren't in the game, though all of the actions played out, they could of had Liberty Prime with them (Imagine: The NCR vs BoS with Liberty Prime).
My biggest question is, even if they got a load of tech, and stayed true to the mission, how could they ever get all of that tech back? They are on the other side of the country, and the road in between is dangerous. Would be even tougher now that the NCR and the Legion are crawling all over the Western United States (at least a small portion of the west). If they hadn't picked up the kids in the Pitt and recruited from the locals, I doubt they would have enough manpower to guard the citadel, collect technology, and transport it all back without taking a lot of loses. Was the BoS going to send vertibirds? Then again, do they even really have any on the West coast, as it seems to be no mention of them with the vertibirds, just the blue prints. I doubt they would literally drag Liberty Prime all the way back to West.
I kinda doubt the NCR knows the Midwest exist. The Westcoast brotherhood barely knows of their existance.
I'm sure if they found a bunch of power armored soldiers, and they just mention in their names "brotherhood of steel", then they would probably attack them.
Edit: To be honest, I think if the NCR heard of large groups of Brotherhood type soldiers in the Mid and East United States, they would have a heart attack.