Larian Studios Forums Divinity: Original Sin 2 - The Modding Dungeon Divinity - Original Sin 2 - Modding General Divinity Engine 2 "Locked by Source Control"

You cannot delete existing objects from a level in a mod. The reason is that the way mods work is:
1) if they contain an object that does not exist in the original level, it gets added
2) if they contain an object that already exists in the original level, the original object gets replaced with the new one (which can be at a different position, have different stats, etc)

There is no support for overriding an object with a deleted version of itself. It could also give issues with scripts that refer to this deleted object. That does not mean it is impossible to remove objects though:
1) if they are scenery items (items with a blue box icon in the items/world outliner view), you can simply drag them outside the level bounds in your mod, so they won't be visible to players
2) if they are dynamic items (yellow box icon) or characters, you can place them off-stage from script. You can also move them out of the level bounds, but then you run the risk that script will teleport them to their original position. Even if you set them off-stage, there is still a small risk that script will set them on stage again at some point, but it is smaller.