The GameObject Brush uses the Prefab system when painting onto the Tile Palette. This allows users to update the original Prefab and get the changes on the painted instances in the Tile Palette.
When the original Prefab is deleted, the user should get the same error notifying that the original Prefab of a painted instance is no longer in the project. Users will have to restore the original Prefab or removed the painted instances from the Tile Palette to resolve this.