So I created a new interior cell and populated it with Raiders. This is my first practice work in the geck. First area I've made, first navmesh, npcs, quest etc.

And in this cell I've reorganized the NPCs and their patrols and changed the layout of the interior a couple of times. Today I learned how to make killing targets a quest objective and that worked out pretty well.

The problem I'm running into is that in the game I loaded an earlier save from before my current setup for the area.
And unfortunately when I did that the game seems to have partially reverted to that earlier setup!
It doesn't make any sense to me. The save game data shouldn't include anything about NPC placement/spawning/patrols etc. all of that is set up in the geck and it should just read the plugin data file and load everything from that so it shouldn't matter at all what savegame is loaded when I enter the area! Right??? With the obvious exception of the savegame being after the quest is completed, which isn't the case, I've been testing and changing the quest all along and haven't made any saves after completion.

But here's the specifics: when I first populated the cell I just threw a bunch of random NPCs into two rooms. Later I added some new NPCs, added a room, evenly distributed the NPCs throughout the area, set up several patrols around the area, gave the NPCs specific reference ids set them as targets for a quest to kill all NPCs. I ran the quest and completed it without saving multiple times and it was working fine. Then I loaded an earlier save and entered the area to try it again. This time, some of the NPCs are where they're supposed to be as per the current status in the geck, all of the new level design made since that save is loaded properly, but most of the NPCs have reverted back to being two large groups with no patrols set up standing around in those two rooms I originally put them in. So it's ignoring most of the data file saved by the geck! I don't know how or why it would recognize the changes to the level design as far as static architecture but then be ignoring the patrols and npc distribution that's in that same data file??? Anyway when I open the level in the geck it shows all of the npc placement/patrols exactly where I left it, but when I load the game it's like I haven't set any of that up!

I've saved the data file. I've closed and reloaded the game and the data file in geck repeatedly. I've restarted the PC. But every time I load the game it's like it's ignoring the current npc placement and going by an older data file that no longer even exists!

I can't just reload the savegame I was using before because that was an auto save which was overwritten when I loaded the older save and entered the area.

Also the quest is broken now. In the data file it's still set such that all NPCs have to be killed to complete it. All the reference numbers and data is just like I left it when it was working before. But now when you entere the area and kill one npc you get the quest completed.

What is going on here and how do I fix it???