This is not too easy. When you move references, you also have to transfer them to the correct cell. Apart from updating object reference locations, you have to move door markers, travel markers, pathgrids, and AI patrol data. You also have to update every script/dialogue result script that directly sets coordinates (e.g. AI escort commands, teleports, placing objects). The last one is probably the annoying part.
Smart Merger already has that working and fixed. Unless I'm missing something, (
like move references which I'm sure are off) everything else should be covered. as part of my documentation example, I raise the http://rtcvb32.001webs.com/SmartMergerDocs/25/move_land.htm and even have a clean looking picture showing the proper gap with everything moved. When you move objects, every land reference of those objects do need to be updated. (
Specifically teleport markers). The only thing
SM doesn't fix in regards to that, is scripts. If I could decode and encode the encoded bytes, I could fix this. Moving tends to break scripts too, requiring them to be re-compiled, but this is a minor issue.
EDIT: AI patrol data... I'll have to look that up perhaps and see if I require any updates.