The flight of Mosiah1 seems to have involved a number of Nephites, maybe a few or maybe many. However, we have to wonder why there aren't any references made by Amaleki, Mosiah1, Mormon or Zeniff about those Nephites who might have stayed behind? Were they automatically classified as Lamanites (see 2 Nephi 5:6,9)? Were they classified as dissenters (see Alma 47:35)?
One other option, according to Sidney Sperry, is that they might have been destroyed according to Jacob's prophecy:
"But wo, wo, unto you that are not pure in heart, that are filthy this day before God; for except ye repent the land is cursed for your sakes; and the Lamanites, which are not filthy like unto you, nevertheless they are cursed with a sore cursing, shall scourge you even unto destruction. And the time speedily cometh that except ye repent they shall possess the land of your inheritance and the Lord God will lead away the righteous out from among you" (Jacob 3:3-4).
A fact indicating that it might apply is that when the expedition of Zeniff and his followers made its way to the land of their forefathers, it was found that Lamanites were in control and that the cities were in a bad state of disrepair (Mosiah 9:6-8). There were no Nephites living there. [Sidney Sperry, Book of Mormon Compendium, p. 276]
Geographical [Theory Map]: Omni 1:12-14 Mosiah Flees from Nephi to Zarahemla (Year 398)