I've checked out the construction setwiki, but I was wandering if anyone had any extra information on this. Does this change the base objects name? If so, is there a way to change an NPC reference without changing the base object name?

How do you properly use this function?

Im not sure what you mean....

Do you mean, if you change the mod's filename, will it effect how it is loaded into the game. In my opinion yes it will, simply because by changing the name, the game recognises it as a different mod, while all the ID's will be the same, it will all be reset as the original mod they are from is no longer being loaded.

OR

Do you mean, can you change an NPC's name without changing it's baseID? in that case no. If you edit a baseID form by going through the reference in the CS when you save the edits you can save it as a new baseID and that reference gets the new baseID.

What I mean is this

http://cs.elderscrolls.com/constwiki/index.php/ModName

If I use modname in a script to rename an NPC ingame, does that change the base id's name?

I've used CreateFullyActorCopy, and successfully changed the copies name without changing the the NPC it was copied from, however, the copy lacks the scripts that the real NPC has...is there any way to add a script to an object in game?