1. Try to ALWAYS save the WHOLE map together, at once. That means that (if you have 1.4SDL) you have to fly through your whole map, load all ADTs and then use FIx gaps (all adts) in Assisst menu, very handy tool for that. It will fix gaps in terrain, obviously, but it will also mark all loaded ADTs as edited, so they will be saved.
2. Do not save your map more then once per running noggit. So if you want to save your work and then continue, restart whole application.
By keeping these 2 rules you should never get any duplication or disappearing problems. If you are editing some part of blizzlike continent, then you have to at least select part which you want to edit and always save the whole part together. Resizing area which is to be modded might give you some troubles with duplications, but if it will, it should not be a big deal at all if you just add a few ADTs into your list of those which should be always edited and then always edit them.
You can also click into ADTs with whatever tool or move some model in them a little bit, if you don't want or can't use fix gaps function.
