They dont usually 'disappear' by themselves. Are you 'Optimizing' the navmesh? It removes too narrow and too steep of areas for NPCs can't navigate.
Nope... I'm not. I honestly have no clue. I move on to a different part of the nav mesh and havn't had any more problems. I'll see if it still gives me issues in a bit.
It actually just happened again. I was working on a navmesh. Hit the Save button, and the navmesh just disappeared.