Problem with map editing.

The issue is that this problem specifically arose with this map; other maps, even larger ones, were edited without any problems or duplicates...

Technically, the problem isn't with the map itself, but with the executable file: it's limited to 2 GB of memory usage. Therefore, huge and incredibly detailed maps quickly fill this limit, causing the game to crash. It could also be a smaller map, but overloaded with objects. Try using a patched executable or the NTCore patching program from the link provided above, create new profiles more often (as save files can contain information from other modified maps), and avoid saving excessively during gameplay. I can't offer any further advice.