Title says it. I'm working on a mod that changes stuff around in the Cistern. I am ready to release it, but I need to find a way to fix this first.
the issue is that a lot of the random baskets and pots that clutter up the area have been removed, or relocated in my mod. If you start the mod with a clean save (as in a character that has never visited the Cistern before), then everything is the way I set it up to be. But if you are playing with a dirty save (guild member), then random miscellaneous stuff will be in its original location scattered around. This also includes some static stuff, furniture, hay piles, and most noticeably the statue of Nocturnal and clutter around the vault. Oh, and the embers from some of the braziers.

Is there any way to make sure that all this stuff stays where it is supposed to?

Sadly ... No.

If the problem is persistance - and I haven't read anyone getting clutter move issues with persistance, but it does sound like that is your problem - then your mod is not Pre-Saved-Game compatible. Though it will be post-Saved-Game compatible

This isn't your fault ... from how you describe it ... somehow, someway, Beth has managed to get some objects/location-of-objects to persist in a saved game and they will then load in those locations when a saved-game that contains those object-positions is loaded ...

Load order is Vanilla -> Mods -> Saved Games (and no way to change that, AFAIK)

(Your mod is not alone in this, either)

This is ridiculous. It messes things up completely. Even items that I have completely deleted are still appearing in an existing save game. Hopefully the modding community figures out how to fix this at some point in the future, it certainly wasn't that way with Oblivion.
Thank you for the speedy reply.

How would making a button that disables the old and enables the new (or old in a new position) and then the button disables itself to set the new state for a new save game state?
It's kind of an obtuse solution, but would that force a new condition?

try not to delete the objects in question, but link them to an enabling parent and set this to "initially disabled".

that would work if I hadn't deleted these objects days ago. Although, it would be long and tedious work, but since every item maintains its own REF ID, if I added in items using the ref ids of the problematic items and then did what you are saying, that would work right?

EDIT: I tried using the ref ids to replace the items, but it doesn't work like that unfortunately. You can assign a specific ref id that is used in the editor, but that won't show up in the game, so my idea is moot. Worth a shot though.