### 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)

if (atlas_source) {
					const TileData *tile_data;
					if (q.runtime_tile_data_cache.has(E_cell)) {
						tile_data = q.runtime_tile_data_cache[E_cell];
					} else {
						tile_data = atlas_source->get_tile_data(c.get_atlas_coords(), c.alternative_tile);
					}
					q.navigation_regions[E_cell].resize(tile_set->get_navigation_layers_count());
					for (int navigation_layer_index = 0; navigation_layer_index < tile_set->get_navigation_layers_count(); navigation_layer_index++) {
						Ref<NavigationPolygon> navigation_polygon;
						navigation_polygon = tile_data->get_navigation_polygon(navigation_layer_index);
						if (navigation_polygon.is_valid()) {
							Transform2D tile_transform;
							tile_transform.set_origin(tile_map_node->map_to_local(E_cell));
							RID region = NavigationServer2D::get_singleton()->region_create();
							NavigationServer2D::get_singleton()->region_set_owner_id(region, tile_map_node->get_instance_id());
							NavigationServer2D::get_singleton()->region_set_map(region, navigation_map);
							NavigationServer2D::get_singleton()->region_set_transform(region, tilemap_xform * tile_transform);
							NavigationServer2D::get_singleton()->region_set_navigation_layers(region, tile_set->get_navigation_layer_layers(navigation_layer_index));
							NavigationServer2D::get_singleton()->region_set_navigation_polygon(region, navigation_polygon);
							q.navigation_regions[E_cell].write[navigation_layer_index] = region;
						}
					}
				}
			}
		}
		q_list_element = q_list_element->next();
	}
}
void TileMapLayer::_navigation_update() {