They are in decline does not mean they are falling apart and almost gone. The war against BoS and NCR probably did spread beyond the Mojave but we have not learned of Lost Hills being destroyed. The fact that NCR's economy went to crap tells me BoS were kicking some butt. Mojave BoS only went into that hole because their leader was a wuss. The War ended and chances are the BoS being allies with NCR will be canon.
The Devs would not kill off the BoS without telling us. DC is a tiny little dot and California is huge. Brotherhood have been around long before NCR and they have built bases all over the place. They could have chapters outside of NCR territory.
Story with Maxson makes no sense then again little of FO3 made any sense. If you are facing trouble in at home why sent the last Maxson across unknown america with only a small company of BoS :glare:
Brotherhood(Original) is still out there it isn't destroyed or barely survived. Who else wouldn't get along well with Elijah and send his chapter to Mojave wasteland.
Second, battle for helios on mojave surely wasn't the first battle between ncr and brotherhood, Colonel Cassandra Moore is said to have survived 4 campaigns against brotherhood back in California.
So surely NCR and Brotherhood have a history.
And about Lyons' chapter... well :facepalm:
EDIT: Sorry didn't see rusina's post already mentioning Moore