Bess will disappear forever if the Chosen One goes down into the Modoc caves (this includes the well and outhouse).
It's actually possible to have Bess join the Chosen One permanently throughout the game by means of an exploit. After she has been slaughtered by Grisham or after one has had the Bess encounter, return to a point in the game where Bess' broken leg has not yet been healed. This can be done by temporarily removing the file Modocmain.sav in the current savegame slot and replacing it with one that was made prior to healing Bess' broken leg. In this file variables regarding Modoc's main street are saved after visiting the area. When one now heals her leg again, she will follow the Chosen One for good instead of just in Modoc. Dialogue with her can also be initiated, allowing one to alter her combat options.