### 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)

}
	}
#endif 
}
void TileMapLayer::_scenes_update_dirty_quadrants(SelfList<TileMapQuadrant>::List &r_dirty_quadrant_list) {
	const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	ERR_FAIL_COND(!tile_set.is_valid());
	SelfList<TileMapQuadrant> *q_list_element = r_dirty_quadrant_list.first();
	while (q_list_element) {
		TileMapQuadrant &q = *q_list_element->self();
		
		if (instantiated_scenes.is_empty()) {
			for (const KeyValue<Vector2i, String> &E : q.scenes) {
				Node *node = tile_map_node->get_node_or_null(E.value);
				if (node) {
					node->queue_free();
				}
			}
		}
		q.scenes.clear();
		
		for (const Vector2i &E_cell : q.cells) {
			if (instantiated_scenes.has(E_cell)) {
				
				continue;
			}
			if (!Engine::get_singleton()->is_editor_hint()) {
				instantiated_scenes.insert(E_cell);
			}
			const TileMapCell &c = get_cell(E_cell, true);