### 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)

const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	ERR_FAIL_COND(tile_set.is_null());
	ERR_FAIL_COND(p_pattern.is_null());
	TypedArray<Vector2i> used_cells = p_pattern->get_used_cells();
	for (int i = 0; i < used_cells.size(); i++) {
		Vector2i coords = tile_map_node->map_pattern(p_position, used_cells[i], p_pattern);
		set_cell(coords, p_pattern->get_cell_source_id(used_cells[i]), p_pattern->get_cell_atlas_coords(used_cells[i]), p_pattern->get_cell_alternative_tile(used_cells[i]));
	}
}
void TileMapLayer::set_cells_terrain_connect(TypedArray<Vector2i> p_cells, int p_terrain_set, int p_terrain, bool p_ignore_empty_terrains) {
	const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	ERR_FAIL_COND(!tile_set.is_valid());
	ERR_FAIL_INDEX(p_terrain_set, tile_set->get_terrain_sets_count());
	Vector<Vector2i> cells_vector;
	HashSet<Vector2i> painted_set;
	for (int i = 0; i < p_cells.size(); i++) {
		cells_vector.push_back(p_cells[i]);
		painted_set.insert(p_cells[i]);
	}
	HashMap<Vector2i, TileSet::TerrainsPattern> terrain_fill_output = terrain_fill_connect(cells_vector, 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 {