I've had similar problems. It's most likely because you've used TCL to disable collision detection when you're within speaking range of any NPC's. I think it's a bug that causes them to behave strangely, sometimes following you when you fly up/down, sometimes not. When you use TCL again to re-enable collision detection, they can fall and die or even fall OUT of the game world altogether if they're below ground level!
I once used TCL at the Siltstrider landing in Balmora to fly up for an overhead view of Balmora. Unknown to me, Hul the Pauper (Female Argonian) had followed me up there. I was admiring the view when she approached me from behind and growled, "What does it want"! Needless to say, there's still a head-shaped dent in my ceiling to this day!
![Shocked :shock:](./images/smilies/icon_eek.gif)
I'm kidding!
As for moving NPC's around, the console provides no way to do it (at least I haven't discovered if there is a way yet). However, you can "fudge" it by killing them then recreating them at a new position. Here are the console commands relevant to your original question:-
Key:
[] = Meaning of abbreviation.
{} = Placeholder for a TES:CS object ID. If it contains any spaces, they MUST be enclosed in quotes, i.e. ID h8_ball (underscore as separator) is OK, but h8 ball (space as separator) must be enclosed in quotes to make it "h8 ball". The ID of an NPC is usually their name in lower case only.
TCL [Toggle CoLlision]
Toggles collision detection disabled/enabled for yourself AND any NPC's within speaking range. Causes strange effects with NPC's sometimes following when you change height, sometimes not. Wandering NPC's can also end up stuck in walls, etc, often completely hidden from view.
Tip: Use TCL to disable collision detection ONLY when you're WELL out of speaking range of any NPC's. I'm not sure what happens if you THEN come within speaking range, since I've stopped using TCL around NPC's because its effect is too unpredictable.
TAI [Toggle Artificial Intelligence]
Toggles AI disabled/enabled for ALL NPC's and Creatures.
Tip: TAI, TCL might prevent NPC's following you up/down when collision detection is disabled, since they shouldn't move with their AI disabled. Once you're finished flying around, use TCL, TAI to reset back to normal. Personally, I haven't tested this since I don't usually use TCL around NPC's.
RA [Reset Actors]
Resets all actors in the current cell back to their original start positions. I have noticed, however, that after casting Command Humanoid on an NPC, they often won't reset. This may be because their original position is now the last position they were at when your last Command Humanoid spell wore off.
Tip: If NPC's seem missing or are stuck in geometry, TCL, RA, TCL will sometimes reset them, i.e. disable collision, reset actors, enable collision. It doesn't always work, though, definitely not if they've fallen and died.
{NPC}->SetHealth 0
Instantly kills an NPC without penalty. Use if they've fallen off a platform or through geometry and are stuck, then use PlaceAtPC to respawn them, preferably somewhere where they won't do it again!
Example: "dranas sarathram"->SetHealth 0
PlaceAtPC {NPC},0,0,0
Spawns an instance of an NPC at your current location, facing in the same direction you're facing. You'll initially be inside them, but all you have to do is walk out of them. Use to respawn NPC's who've fallen and died, or those you've killed.
Example: PlaceAtPC "dranas sarathram",0,0,0
If all else fails, use SetHealth 0 to kill an NPC, then PlaceAtPC to respawn them again at (or near) their original position.
Finally, for completeness,
PC Console Commands - Full Listing
Hope this helps.
Edit 1: People have posted while I was editing. There's no mention of the Position command in the full list but, if it works, by all means use it.
Edit 2: Aha! Found it in the modding section of the Wiki!
TES3Mod:Position. Personally, I find it's easier to just use SetHealth 0 then PlaceAtPC, which respawns them AT your current position without needing to learn any coordinates.