It is well known problem. There isn't way to fix it at all, but there is a way to not have this happening anymore. Save only once per running application. Whenever you save your progress, always restart application before making any other edits (and saves) to your zone.
I would also suggest you to always save the whole zone you are editing together. Fix gaps (all ADTs) in Assist menu is the best tool for marking all ADTs on map as edited.
So, to avoid any saving bugs:
1. run noggit
2. fly through the whole zone, so all ADTs are loaded (well, this won't be possible in blizzlike continents, I know...)
3. use Assisst -> fix gaps (all ADTs)
4. do your edits, whatever you wish
5. save
6. close noggit
7. repeat the whole process if you wish to continue with another edits after saving