I doubt the Brotherhood would just hole up in the bunker and wait for the NCR to show up. Far more likely they'd establish a defensive perimeter well outside the bunker. NCR still has the advantage in the long term but pushing back entrenched troops in power armors is going to be a long and bloody process.
That or launch a massive offensive strike to keep the NCR on the defensive and maintain the initiative. That seems too bold for the Brotherhood leadership though.
Perhaps the BOS will still be able to control their headquarters at Lost Hills. But the thing about the Brotherhood is that unlike the NCR, the Shi, or even the Legion, they are a military organization and lack a civilian government. They don't have any formal borders or territories, only outpost and bunkers. Their lack of a home front means that their supply lines can easily be cut off if they loss the support of the territories that the branch is in.
In Fallout 1, it is said that the BOS support themselves at Lost Hills by trading guns with caravans at the Hub. With the war with NCR, I don't see how they can continue to support themselves.