NI doesn't hold your hand if you're new to editing the IE or some part of it, so you can really mess things up. I like it because it doesn't limit me like other editors tend to do, and I know my way around filetypes, or can figure them out when the need arises. While the interface can be tedious at times, I still prefer it over DLTCEP's.
Lots of things can happen when you move an area, since references to various other files can break if those files aren't moved as well. AREs can refer to WED files (header), CRE files (Actors, Spawn Points, Rest Spawns), ITM files (Containers), BCS files (header, Actors, Info/Trigger Points, Containers, Doors), WAV files (Ambients, Doors), DLG files (Doors), and BAM files (Animations). There are also a host of string pointers into dialog.tlk, but it won't break the area if these point to incorrect or missing strings. There is also a MOS file for the overhead view and various BMPs for path searching, lighting, height calculation and so on.
You should be able to remove safely most things except doors, and their associated exits, in ARE files. I only remove doors if the WED file being used doesn't support them, as is the case in some of the dream sequence maps in BG2, which have leftover artifacts from when the maps were copied from BG1 and edited.
Probably the best way to move an area is to load it up with IETME, which extracts all the pertinant files (ARE, WED, TIS, MOS, BMPs), then copy those to your target override folder. Then you can edit the ARE and remove the aforementioned things that give the area 'life'.
The latest beta of NI is better than the latest non-beta release, in some editing aspects, so you might consider that if you don't have the beta. Supposedly Jon Olav will get back to work on NI "soon", as he's got a pile of bug reports and feature suggestions sitting in his inbox.