If Navarro was destroyed, and you had the NCR and BOS on your heels, you would run about as far away from them as possible. The Vegas remnants travelled there by Virtibird, but that doesn't mean the rest of the Navarro-ites travelled by Virtibird. They could have caravanned it , to find a new settlement.
The Vegas Remnants can't have travelled by Vertibird I don't think, Doc Henry was a deserter who was living in the NCR at the time when Fallout 2 started and had his own little laboratory; which seems more likely, the Remnants found him by accident after Henry too fled the NCR after they became suspicious of his rather specialised and specific fields of science (neurology & cybernetics) around the time when the NCR began looking for Enclave survivors to arrest, or, that Whitman landed her Vertibird somewhere (again, amid the waves of NCR trying to find them and Henry just happened to be there.
Besides here a thought, most of the Navarrans were simply killed in the battle; had the same thing yesterday I think, somebody said "Well I don't see how they got all of their civilians from Raven Rock to Adams Airforce Base", did you ever consider that they just died when the BoS stormed the place or the LW destroyed it?