Given that the location of Lost Hills has never been a secret, some of the most uneducated of Hubites were able to point you in the direction of it and Cabbot confirms that they trade with Merchents; I'd say that it surely must have been attacked by the NCR.
It depends on when the war started though really, I mean it took probably at least 8 years after Fallout 2 for them to destroy Navarro. I'd say it's unlikely that Lost Hills still remain; given the Brotherhood's track record in the Mojave about going down with their bunkers I'd hazard a guess that the High Elder's and most of the personnel relocated and left behind a token force.