Godot swapping assets

I’m using Godot 4.2.1 on Linux

I’m having trouble understanding placing assets in the 3D view in the editor. I’ve had this problem several times now, where if I have the editor open and I re-export and overwrite some 3D assets that are already placed in a scene, Godot will swap out certain instances of models with others if I restart the editor. The instances swapped are not related to any of the ones that were replaced.

Am I doing something wrong, or is this a bug? It feels a bit like a bug.

In the editor:

Same asset after restart: