The Western BoS are at the Lost Hills bunker in California (or where ever they are hiding now from the NCR). The Mojave chapter is just a smaller group that went off with Elijah. Elijah and McNamara were/are just Elders, not a High Elder, so there should still be other chapters elsewhere.
They are still the Original BoS just a Chapter of it. They still follow the BoS Codex unlike Lyons and the MWBoS. The Brotherhood span (or once did) all over California, from Lost Hills to the Den in the North. They might have even had their own state within NCR.
We already have the Western BoS, what do you think the Mojave Chapter is? Do you mean the MIDWestern BoS? If that's the case, we'll likely find a corpse or two referencing it, but as for the MW BoS PA, it's a no go, seeing as Obsidian weren't allowed to add new PA into OWB, I highly doubt they'd be allowed to add PA in LR.
I am hoping for a refrence of the http://www.youtube.com/watch?v=GtXhuaTcohY in the new DLC. I would love to see live members but I will just be happy to see some dead ones. A couple skeletons dressed in leather armour, next to some rusted Calculator Robots, such as a Behemoth.
Caesar’s Legion captures Brotherhood in their eastern territory. The Legion only goes as far east as Colorado. The Midwestern Brotherhood made it as far as Colorado Springs. Drawing a conclusion from that, the Midwestern Brotherhood must still be in Colorado. So I am hoping for another one in Lonesome Road. The name Barnaky popping up would just be :drool: