Does anyone know how to "reset" all the persistent references that have been moved during the modding process?

They're fine in the CS, but when played in the game they're back in the original positions. I've read that a script is needed to make the game see the changes, but I don't know what that would be.

These references are for things like doors, the fire in the Anvil lighthouse and it's cauldron, and the dark brotherhood barrel that's used as a drop.

Did not quite understand the scenario:

Do you mean you moved the lighthouse fire and it is back to the vanilla position?

Or you moved it to position A, then to position B and, in game it is back to position A?

Yeah the first one I guess.

What I've done is expanded the harbour and so I had to move the lighthouse. In the CS everything is where I've placed it, but when run in the game they're all back in their vanilla positions.

Well . . . just created a new esp, moved the lighthouse, changed the landscape a bit, saved, activated the esp and entered the game : everything was correctly changed as I did in the CS.

Meaning . . . there is nothing special about the lighthouse

The only suggestion I have is that you make sure you load a clean save (a game saved without your mod) because sometimes the position of an object is saved in the save game and, as the saved game is loaded after the esp, it overrides any change you made in the CS.

Starting a new game fixes the problem. Now the problem is when the mod is ready for release, does that mean everyone who uses it will have to start a new game?

No.

Try loading any of your own saved games, saved before you started the mod and you see it will work.

You may also do the following:
1 - Deactivate your mod
2 - Load the last saved game (the one that was not working)
3 - Save again (as your mod is not active, the changes to the lighthouse will not be in the saved game)
4 - Activate your mod
5 - Load the game saved in step 3
6 - Your changes in the CS should be fine now

Keep the saved game saved in step 3 and use it to test your mod from now on.

The correct way to move object once it becomes part of the players saved game is to delete it and replace it with a new one. That forces it to update the save and moves the object in the game be it a new game or an old game.

Scripted objects must be persistent and must be moved that way too, otherwise they remain where the player first saw them.

Btw I use that trick a lot, especially in kvatch aftermath so i am very familiar with it.

That should be what you need to know.

Edit:

Since this is for a city mod I will explain something else. Deleted items automatically return if the mod that disabled them is later removed. So to allow people to uninstall your work later safely, you should delete and replace that item, not disable. Disabled items remain disabled in players saves even if the mod is removed.

Quest makers need to know this stuff, its quest making 101 but the trick will help you too.

BTW it helps other mod makers if you keep the original street layout and it helps the AI if the streets are wide and mostly clear. AI path finding has not improved much in 18 years.

PS pm me here if you need any further advice, I do not mind helping modders if they need it

Giskard

This up here ^ is good advice.

I had similar problems as you are experiencing when working on house mods - clean saves would be fine, but any character that had previously entered the house would see various objects out of place. I tried any number of scripts to force disable/re-enable parents & persistent refs in-game, but ultimately the above solution was the only thing that solidly worked. Copying then deleting objects, then pasting them back in place (CTRL + SHIFT + C) works quite well for this & ensures they land where they started in the CS. Since they'll have new ref IDs, wherever you move them is where the player will see them, because the cached data in the save game won't include that ref ID.

To take it a step further, the number of children a parent object has is also cached in a save game (very frustrating when modding a vanilla house, since most objects are parented for the furniture purchase scripts). So giving all objects a new parent (meaning a new object, not just using an existing one as a parent) will force the game to display them.

Learning these tricks is the only reason I'm willing to open up the CS at all anymore, because you can't predict or control what data is cached in player's save game, and they will still blame you for floating & colliding objects. /sigh lol