Do not save multiple times per running application. After every save restart noggit. Also try to save whole location everytime together. Open map, fly through it so you load all ADTs, in Assist menu choose fix gaps (all ADTs). Thats the easiest way how to mark all ADTs in your map as "edited" and thus saved. Saving only a part of map should not lead to disappearing models, but it can lead to duplicating them.
