The UOP Citadel Hall fix replaces all the CitadelHallDoor01Anim instances in the game with a revised one to fix a sound bug, but as a side effect repositions the door. So it also moves the doors back into place, at least the ones in the vanilla game.

The problem arises if a mod uses the mesh, as these now get the modified one with its offset origin, and they aren't where they were placed in the CS.

I'd like recommendations on how to accommodate this in a mod that has CitadelHallDoor01Anim instances. I can detect if the patch is present, and script repositioning the doors, but that means making them persistent references, which may have side-effects I haven't thought through. I can clone the original mesh and use my copy instead, so that my doors aren't CitadelHallDoor01Anim any more, and they stay where I put them. I can tell users not to use that part of the UOP with my mod (since it's a separate esp they can just uncheck).

Any opinions? And are there other mods that have done anything similar?

I'm not sure how many people are using that fix anymore. I guess there are still quite a few, but I know I don't bother anymore and I've seen several posts that tell people not to bother.

I would recommend you go with cloning the doors and using your version. That sounds to me like it would be the best way to avoid issues. It will also make things cleaner should people decide to uninstall your mod.

You could probably look at Open Cities Classic - I'm pretty sure Arthmoor cloned all the doors when he opened up the city spaces.