### Godot version

4.0 stable

### System information

Windows 10

### Issue description

Running .clear() on a TileMap with Scene tiles leaves the tiles in place, as though nothing happened.

This appears to be the same issue as raised in [#69596](https://github.com/godotengine/godot/issues/69596), [#72456](https://github.com/godotengine/godot/pull/72456), and [67330](https://github.com/godotengine/godot/pull/67330). None of the previous issues seem to have presented a fix for this issue besides running some dummy operations on the TileMap, which have not had any effect for me.

Manually running queue_free() on each tile scene doesn't work, presumably since they are being cached. And running a dummy operation on the TileMap doesn't have any impact to speak of.

Not sure how to proceed, or if it's just impossible to remove Scene tiles once they're created.

### Steps to reproduce

The minimal reproduction project has a TileMap with several simple scene tiles. The attached script attempts to .clear() the TileMap when the user presses Enter, demonstrating my issue.

### Minimal reproduction project

[TileMapMinimumRecreationProject.zip](https://github.com/godotengine/godot/files/10959111/TileMapMinimumRecreationProject.zip)

}
	HashMap<Vector2i, TileSet::TerrainsPattern> terrain_fill_output = terrain_fill_path(vector_path, p_terrain_set, p_terrain, p_ignore_empty_terrains);
	for (const KeyValue<Vector2i, TileSet::TerrainsPattern> &kv : terrain_fill_output) {
		if (painted_set.has(kv.key)) {
			
			TileMapCell c = tile_set->get_random_tile_from_terrains_pattern(p_terrain_set, kv.value);
			set_cell(kv.key, c.source_id, c.get_atlas_coords(), c.alternative_tile);
		} else {
			
			TileSet::TerrainsPattern in_map_terrain_pattern = TileSet::TerrainsPattern(*tile_set, p_terrain_set);
			TileMapCell cell = get_cell(kv.key);
			if (cell.source_id != TileSet::INVALID_SOURCE) {
				TileSetSource *source = *tile_set->get_source(cell.source_id);
				TileSetAtlasSource *atlas_source = Object::cast_to<TileSetAtlasSource>(source);
				if (atlas_source) {
					
					TileData *tile_data = atlas_source->get_tile_data(cell.get_atlas_coords(), cell.alternative_tile);
					if (tile_data && tile_data->get_terrain_set() == p_terrain_set) {
						in_map_terrain_pattern = tile_data->get_terrains_pattern();
					}
				}
			}
			if (in_map_terrain_pattern != kv.value) {
				TileMapCell c = tile_set->get_random_tile_from_terrains_pattern(p_terrain_set, kv.value);
				set_cell(kv.key, c.source_id, c.get_atlas_coords(), c.alternative_tile);
			}
		}
	}
}
TypedArray<Vector2i> TileMapLayer::get_used_cells() const {